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Glossary of Terms
Companies that are very similar to the company being valued. These companies will most likely be direct competitors and will offer the same or very similar products or services to a similar geographic or demographic consumer base. These companies should have similar operating margins, such as Profit Margin and Return on Equity. ValueMyStock's Valuator™ formula uses the stock prices and price-to-performance ratios of your selected comparables to calculate the intrinsic value of your stock. Learn how to find quality comparables
Growth Investing
Purchasing a stock with the expectation the price will increase without regard for the true value of the stock. Reasons for purchasing a growth stock include market momentum, analyst's future price projections, new product lines or market capitalization. Growth Investing is the opposite of Value Investing.
Day Trading
Purchasing a stock for the purpose of holding that stock for a very short period. Most day traders are in and out of a position within the trading day, hence the term "Day Trading." This form of speculating seeks to profit from the daily ups and downs of market volatility without regard to the intrinsic value of the stock.
Intrinsic Value
The price that a stock should sell for if properly priced in a normal market. Also described as the true value of a stock.
Margin of Safety
A threshold that Value Investors place upon their stocks before purchasing. ValueMyStock recommends a minimum Margin of Safety of 30%, meaning that the selling price should be at least 30% less than the intrinsic value before the stock is considered undervalued.
Price-to-Performance Ratios
These are ratios that allow investors to quickly compare the performance of a stock to it's current price. Ratios used in our Valuation by Multiples formula include:
- Price-to-Earnings (P/E)
- Price-to-Sales (P/S)
- Price-to-Book Value (P/BV)
- Price-to-Cash Flow (P/CF)
- Price-to-Earnings Before Interest, Taxes, Depreciation and Amortization (P/EBITDA)
SEC Filings
Financial reports and other documents every publicly-traded company must submit to the Securities and Exchange Commission. Reports often used by Value Investors include 10-Q (filed quarterly) and 10-K (filed annually) reports. These reports are often found on a company's website or through FreeEDGAR.
Selling Price
The current price a stock would sell for in the open market. Also known as the Bid.
Value Investing
Purchasing a stock that appears underpriced based upon current and historical performance and the prices of the nearest competitors and selling the stock once it reaches intrinsic value.


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Tobias and the Angel Poster
This poster print features Andrea del Verrocchio's Tobias and the Angel.
The subject is taken from the apocryphal Book of Tobit. Tobias was sent by his blind father, the merchant Tobit, to collect a debt. 'Ricordo' (memorandum) is written on a small scroll in the boy's hand. The Archangel Raphael who accompanies Tobias instructs him to extract the heart, liver and gall from a fish as a cure to heal his father's blindness. Raphael is shown holding a small box containing the remedy.
The story of Tobias and the angel was a popular subject in 15th-century Florence, where a confraternity of Saint Raphael flourished. Raphael was venerated as a protector of travellers and as a healer. The theme of filial piety, enterprise and charity was important for the merchant families of the city.
It is likely that more than one artist worked on the painting, consistent with practice in Verrocchio's workshop. Some parts - most notably the dog - have been plausibly proposed as the work of the young Leonardo.
Tobias and the Angel by Andrea del Verrocchio was the focus of the Take One Picture schools course, 2009/10. Take One Picture looks at ways of using paintings in the classroom as a starting point for delivering many areas of the National Curriculum. This principle aligns closely with the DCSF Primary National Strategy: Excellence and Enjoyment, which supports a holistic approach to the curriculum by exploiting the links between subject areas.
About this painting
Tobias and the Angel, about 1475
Tempera on poplar, 83.6 x 66 cm
© The National Gallery, 1867
This poster has a classic white border and the National Gallery logo.
Find more like this:Tobias, Angel, Poster, Andrea del Verrocchio.
Product Information
|Product Code
|Andrea del Verrocchio
|80 x 52 cm
|FSC Paper
|Tobias and the Angel
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Culinary Trends and Fish
Various culinary trends predictions for 2013 have stated that non-traditional types of fish will make their way onto more and more menus throughout the year. Branzino, Arctic Char, and Barramundi are a few types that are gaining widespread popularity. Their abundance makes them top candidates for fish dishes, by keeping their prices relatively low (though pricing depends on many other factors as well). Their versatile preparation methods and flavoring options make them ideal for vegetarian entrées (for those vegetarians who eat fish) or lighter entrée options.
Why is sustainable fish such a big deal? With global warming, the temperatures of bodies of water are rising, becoming less ideal for many types of fish, and causing their numbers to decrease. Fish farming allows the industry to artificially create the optimal conditions for fish to grow, regulating the prices and availability of those fish in the market. Some consumers are hesitant to purchase such fish, due to the use of antibiotics to keep the fish healthy. However, suppliers that raise fish by fish farming, specifically for the purpose of being consumed, are providing sustainable fish, in contrast to fishing from the dwindling numbers in natural bodies of water. Branzino, Arctic Char, and Barramundi are considered sustainable fish. In addition to being top candidates for main ingredients in a vegetarian or non-meat dish, they can be prepared in various ways, incorporating culinary trends related to cooking methods, healthy eating, and sustainable food.
Branzino, also known as European sea bass, is the second most farmed fish after salmon. Its firm, white meat has a delicate flavor. Its small size makes it great for pan-frying, baking, grilling, and steaming, whole or in filets. In the past years it has become a staple of casual and fine dining restaurant menus. In comparison to possible alternatives such as red snapper and black sea bass, Branzino has more steady availability and pricing due to it being farm-raised.
Arctic Char
Arctic char is often compared to trout and salmon. Its flesh ranges from pink to red, and its fat content is similar to sockeye salmon. Its size lends itself to preparation as filets and steaks. The heart-healthy oils in the fish and its high rating as sustainable food combine predominant culinary trends.
Like the first two types of fish described, Barramundi is also a very sustainable food. This white fish has a mild flavor and fat levels that fluctuate from fish to fish. Its size, like Arctic Char, makes it best suitable for preparing as filets, though smaller ones are available as well, and delicious baked whole.
How to Cook Fish
Branzino, Arctic Char, and Barramundi can be cooked in many ways. The obvious options include baking, pan-frying, and grilling. These fish can also be used to prepare fish carpaccio, a twist on the classic beef filet dish, in which the vinegar content will slightly cure the fish. They be cooked in a bamboo steamer, wrapped in exotic leaves, as well. Surprisingly impressive results can be achieved when microwaving filets without skin, as the even cooking of the ingredients allow the fish to be evenly cooked through to a moist doneness. The dish options for incorporating Branzino, Arctic Char, and Barramundi are vast and allow a lot of freedom for creativity and experimentation. With the stable prices and availability of these sustainable fish, and the rising culinary trends of healthy eating and non-traditional fish on menus, they are a great ingredient to add to the supply list.


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Grand Theft Auto: Liberty City Stories (2005)
Video Game | Action, Comedy, Crime | 24 October 2005 (USA)
Ratings: 8.1/10 from 2,741 users
Reviews: 8 user | 4 critic
There a million stories in Liberty City. This one changes everything. Toni Cipriani, a once trusted guy, is sent to lay low after killing a made man. Now, back to set things straight, he ... See full summary »
Directors:Navid Khonsari, John Zurhellen
Writers:Lazlow Jones (radio station scripts), Dan Houser, 4 more credits »
|Watch Trailer 0Share...


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November 24, 2015
HUSTONVILLE, Ky. (WKYT) - A Boil Water advisory has been issued for areas in Hustonville.
The advisory is in effect for the areas of black Pike, Carter School Road,
Community Center Drive and Highway 2141 from 4600 to Harris Creek Road until further notice.
The advisory is due to a break in a 4 inch line and will be effect until further notice.
Click Here to access the online Public Inspection File
Viewers with disabilities can get assistance accessing this station's FCC Public Inspection File by contacting the station with the information listed below. Questions or concerns relating to the accessibility of the FCC's online public file system should be directed to the FCC at 888-225-5322, 888-835-5322 (TTY), or email@example.com.


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To delete a section which you don't want to print, click on the red highlight or red X. To restore the section, click on the green arrow icon in the upper right hand corner of the post.
Calling all of you who have New Year's Resolutions to eat healthier in 2013! Well, you may want to head on over to Amazon.com where you can snag this Ozeri Pro Digital Kitchen Food Scale for ONLY $11.37 – down from $39.95! Just add this scale to your cart (in silver only) reduced to $18.95, then head to to checkout and you will see at the final stage that an additional 40% has come off (only if you add the silver scale to your cart) – bringing your final cost to only $11.37! Plus, this scale ships FREE within 2 days with Amazon Prime or on orders of $25 or more with Super Saver Shipping.
This seems like a great deal to me for a high quality food scale! Hurry to order, as I'm guessing this scale will either go back up in price or sell out.
(Thanks, Clip & Follow!)


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Ohio State junior forward Deshaun Thomas was selected as a member of The Associated Press' preseason All-America team.
- Filed Under
Aaron Craft can solve a Rubik's Cube in seconds. But can he figure out the 2012-13 Ohio State men's basketball team before the season starts?
"There are no great teams in October," the junior point guard said at this year's media day. "Everyone has to start off at square one."
Ohio State is a confounding group this season. How can a team with so much back from a Big Ten championship and a Final Four berth have so many question marks? ...


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Disability Equality Scheme Pictorial
What is a Disability Equality Scheme?
The Disability Equality Scheme tells you what Birmingham City Council will do to make sure disabled people have the same chances as everyone else. The Scheme has a three year Action Plan (1st April 2007 - 31st March 2010) - an outline of key areas against which Directorates will identify targets following the consultation processes, is included within the scheme.Why are we producing a Disability Equality Scheme?
The Law called the Disability Discrimination Act 2005 required us to produce a scheme.What are the main aims of the Scheme?
* To show how we involved disabled people in putting together the Disability Equality Scheme
* To help the Council think about what is important to disabled people
* To set out the key steps that Birmingham City Council will take to promote disability equality
* develop services to meet disabled people's needs
* ensure that equal opportunity is given to every one
* ensure disabled people are not bullied because of their disability
* make it easier for disabled people to live, work and visit the City.
This means that access to the city must be made better
Nine Key Areas
There are nine key areas in the three year Action Plan:
* Involvement
* Information
* Care Services
* Accessible Housing
* Education
* Employment
* Transportation
* Access to the environment
* Involvement in community activities
The Disability Equality Scheme is due to be replaced with a framework document later this year.


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34 Recent Deviations
Featured: Somnolence
Flight of Ravens in Dark LightA silver veil is drawn over the worldFlight of Ravens in Dark Light by AzraelDarkAngel540
Calling mortals to the world of dreams
Lulling them to sleep with her lure
A Dreamweavers sedative lyre
A cordial of sweet poison
A nightingales velvet dirge
That arises with the music of the stars.
And from the ends of the earth
Trailing from the far North
I see a flight of ravens,
Shimmering in dark light
A fist of black dust
Pitched in the cruel winds
They come to take my soul away
To the twilight cave of Urd
And tear my heart out at my behest
Never shall I know the curse of romance
That ties me down
And makes of me a fool.
Reborn in the fires of pain
I transcend the marble bridge
And with wings of shadow
I join the flight of ravens
In their nocturnal vigil
Bathed in the cold hardness of twilight
I become one with the silver veil.
Relationships- How ready are you?Well at some time you come to a point where you realize your life is not what you planned it to be, or it doesn't completely fit with the image in your mind. There are a myriad of reasons why this happened one of them is being imprisoned by your own past. Think about it, if you live with fears, with doubts, with regrets you are living with the ghosts of your past. Tell me what brings about fear? It is either because you never tried it and you prefer to stay in your comfort zone, or because on the other hand, you tried it and saw an outcome which you were not really amused about. So now what to do? Well usually we end up imprisoned unconsciously and sometimes it is really hard to realize it, let alone admitting it.Relationships- How ready are you? by naamahpammy
So like me for example, I suffer a lot from trust issues because of what happened with my ex. I didn't realize I had such serious trust issues until it hit me, and it hit me in a funny way. I always thought my fears were rational, that I was being mature by remind
Elusion of a dreamI have seen you from my film of silenceElusion of a dream by chiara-scicluna
Broken up believer, too proud to beg
You want to pick up your love and run away -
too many disappointments, in too little time.
Blue eyes speak of shredded hopes
dreams unravelled from the seams
cold ash blown away.
I know that the butterflies have long perished
but a heart still beats
Joy, it now eludes us
but this is not the time or place.
Someday, it will be the time and place.
Don't wanna be youYou, with your fake smiles and trialsDon't wanna be you by chiara-scicluna
with your humourless laughs
fingers slipping their grip
and hollow friendship
with your empty, colourless soul
all you've got is a hole
It's a shame I'm the one doing the crying
I'm the one doing all the trying
You'd think that the blankness within
Would somehow by now have crept in
and destroyed your sugar coating
dissolved it until only pale sweet water remains
While I stand at the side with a history of pain
my heart with a heavy, sore and sorry stain
simply because I was fooled by the reflections of the rain
I believed that you knew what the world was and was not
Turned out I was blinded by the bright lights
and the expensive talk.
So now can you look at me in the eye, all your curtains
have fallen, all the bridges have burned
Your luck turned, heart's been left bare
Look who's losing now.
|More Journal Entries


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Downtown Inc partners
Downtown Inc is proud to partner with these community-minded businesses and individuals. Their support helps build downtown York as a dynamic metropolitan center valued as the heart of the region. We also wish to extend our gratitude to those who choose to partner anonymously.
To learn more about Partnership Opportunities, check out our Partnership Brochure (PDF).
Click here to learn how you can benefit Downtown Inc and save money on your natural gas and electric bills through our partnership with Shipley Energy.
Super Hero - $10,000 and above
Mr. & Mrs. Louis J. Appell, Jr.
Better York
The W. Dale Brougher Foundation
Glatfelter Insurance Group
Kinsley Construction
M&T Bank
PNC Foundation
Shipley Energy
The Stewart Companies
Susquehanna Pfaltzgraff Foundation
WellSpan Health
York College of Pennsylvania
York County Community Foundation
YCCF Women's Giving Circle
York County Economic Alliance
York County Industrial Development Authority
York County Solid Waste Authority
Hero - $5,000 and above
Fulton Bank
PNC Bank
Carolyn Steinhauser
Coni Wolf
York County Chamber Foundation
York Revolution
Benefactor - $2,500 - $4,999
The Beer Ace
Stock and Leader
Sustainer - $1,000 - $2,499
Brockie Health Care
C.S. Davidson, Inc.
Linda & Dave Davidson
FirstEnergy Foundation (Met-Ed)
Gavin Advertising
The Graham Foundation
Jeff & Stacey Hammel
William Hoffmeyer, Esq.
Bill & Kim Kerlin
Martin Library
Ralph Serpe & Bryan Tate
Patti Stirk
Wagman Construction
Advocate - $500 - $999
gift in honor of Louis & Jody Appell
Barley Snyder
Jason & Jody Chesla
CORE Design Group
Kevin Cramer
Krista & Michael Darr
Lewis Delauder
DOCEO Printing
Tim & Joan Fulton
Hammer Creek Enterprises, LLC
Katherman, Briggs & Greenburg
The Left Bank Restaurant & Bar
Eric & Kendall Menzer
Murphy & Dittenhafer
Bob & Donna Pullo
ROCK Commercial Real Estate
Royal Square Development
John Schmidt
Joan Stauffer
Downtown York Subway Restaurant
Transportation Resource Group, Inc.
York Traditions Bank
Associate - $300 - $499
ASCOM, Inc.
The Art Institute of York
Bair's Chicken
Bergdoll & Company, LLP
Brewery Products
Cherie Anne
Christ Lutheran Church
Episcopal Church of St. John the Baptist
Family First Health
John Finlayson
Gallery B
Garden Club of York
Grace Manor Bed & Breakfast
Healthy World Cafe
Michael & Louise Heine
Johnson, Mirmiran & Thompson
Joy's Cafe
Junior League of York
Stephen & Susan Lazun
Kim Lentz
Barbara Linder
Minnich's Pharmacy
Monarch Products Company, Inc.
RSB & Associates, P.C.
Chad Shaw & Mindy Noll
Quaker City Paper
Judy Simpson
Elsie Smith
Strand-Capitol Performing Arts Center
Sweet Melissa's Dream
The Watchmaker's Daughter
YMCA of York and York County
York Academy Regional Charter School
York County Convention and Visitors Bureau
York County Heritage Trust
York Saint Patrick's Day Parade
York Young Professionals
Booster - up to $299
gift in honor of Louis & Jody Appell
gift in honor of Mandy Arnold
Alternative Therapies
Mary Anne & Charlie Bacas
Diane Baker
Barton Associates
Judy Blakey
Blakey, Yost, Bupp & Rausch, LLP
Patrick Brubaker
Buchart Horn/BASCO Associates
Business Information Group
Matthew Carey
Central Family Restaurant
Child Care Consultants
Gayle Cluck
Colony Papers, Inc.
William & Sandra Cooley
Jim Coombes
Lynne Danyo
Ann Davis
DiCarlo's Pizza
Sally & Ron Dixon
Chloe Eichelberger
Meagan Feeser
Law Offices of Christopher Ferro
Michelle Frye
F.W. Behler, Inc.
Gettle & Veltri
Andrew Gobel
Robert Godfrey
Steve Gohn
Grace and Hope Mission
Griest, Himes, Herrold, Schaumann, Reynosa LLP
Kristine Gross
Linda Hess
George & Martha Hodges
Lynn Jensen
Kenneth Johnston
Sue Ann Kline
Dennis Kunkle & Julie Kemper-Kunkle
Ken Martin
Shonna Ilgenfritz & Susan Newcomer
Ken & Margaret Jelonek
J.R.'s Fresh Cut French Fries
Fran Keller
Leadership York
Lise Levin & Bruce Bushwick
Dr. Mary & Mr. Chris Meisenhelter
New Level Advisors
The Newton Group
Henry & Barbara Nixon
Danielle Passaro
Ron & Debbie Perry
Genevieve Ray
Reisinger Poultry, Inc.
Tom & Peggy Selway
Bradley Smith
Shary Smith
Dr. Luther & Mrs. Ruth Sowers
Susquehanna Real Estate
Karin Swartz
Julian Tolbert
Weinstein Realty Advisors
Natalie Williams
York Friends Meeting
Amy Zeigler
Pam & George Zerba


text:
100+ locations
Click to view Walmart's commercial solar project >
Irwindale, CA – 3.2 MW
Click to view MillerCoor's commercial solar project >
San Jose, CA — 650 kW
Click to view eBay's commercial solar project >
22 Sites in Colorado
Click to view Walgreen's commercial solar project >
King Estate Winery
Eugene, OR — 974 kW
Click to view King Estate Winery's commercial solar project >
Sierra Toyota
Lancaster, CA — 617 kW
Click to view Sierra Toyota's commercial solar project >
Heritage Paper
Livermore, CA — 528 kW
Click to view Heritage Paper's commercial solar project >
Montna Farms
Yuba City, CA — 394 kW
Click to view Montna Farms' commercial solar project >
British Motors
San Francisco, CA — 287 kW
Click to view British Motors' commercial solar project >
GAL Manufacturing
Bronx, NY — 237 kW
Click to view GAL Manufacturing's commercial solar project >
Batth Farms
San Joaquin Valley, CA — 1.5 MW
Click to view Batth Farm's commercial solar project >
Maui Art and Cultural Center
Kahului, HI — 463 kW
Click to view MACC's commercial solar project >
Hewlett Packard
Palo Alto, CA – 1 MW
Click to view HP's commercial solar project >
Advance Auto Parts
Connecticut - 1.17 MW
Click to view Advance Auto Parts's commercial solar project >
California - 1 MW
Click to view Directv's commercial solar project >
A solar power system is customized for your home, so pricing and savings vary based on location, system size, government rebates and local utility rates. Savings on your total electricity costs is not guaranteed. Financing terms vary by location and are not available in all areas. $0 due upon contract signing. No security deposit required. A 3 kW system starts at $25-$100 per month with an annual increase of 0-2.9% each year for 20-30 years, on approved credit. SolarCity Corporation will repair or replace broken warranted components. CA CSLB 888104, MA HIC 168572/EL-1136MR, other contractor licenses. All loans provided by SolarCity Finance Company, LLC. CA Finance Lenders License 6054796. SolarCity Finance Company, LLC is licensed by the Delaware State Bank Commissioner to engage in business in Delaware under license number 019422, MD Consumer Loan License 2241, NV Installment Loan License IL11023 / IL 11024, Rhode Island Licensed Lender #20153103LL, TX Registered Creditor 1400050963-202404, VT Lender License #6766.
Savings based on residential PPA and lease customers with at least twelve months of billing data. Savings Rate calculated by subtracting PPA or equivalent lease kWh rate from relevant utility kWh rate. Savings calculated by multiplying actual kWh supplied by SolarCity in customers' first year times Savings Rate. Excludes fully or partially prepaid contracts.
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text:
Fear of the dark: regulating the film experience.
Cronin, Theresa (2007) Fear of the dark: regulating the film experience. Quest (4).
Full text is not in this repository.
|Item Type:
|Additional Information:
Proceedings of the Quest Conference 'Perspectives on Power' 2nd and 3rd March 2007.
|Research Areas:
|A. > School of Media and Performing Arts > Media
|ID Code:
|Useful Links:
|Deposited On:
|03 Feb 2010 06:07
|Last Modified:
|10 Mar 2015 15:50
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text:
Portable Oxygen: A User's PerspectiveWhat Do the Numbered Settings
Really Mean?
Mary in PA and a number of others who use portable oxygen have written to me as follows:
I have a question about the pulse settings on my portable oxygen system. I have heard that the numbers on the pulse dial are not the same as the numbers on my concentrator. Do you know what the equivalent is for say 2 Lpm continuous flow and setting 2 on a pulse dial?
Hi, Mary,
You have raised an interesting question, one that I have heard often from other users of pulse-based systems, I usually get these questions when these users discover that, even when set to the same number, their concentrators supports them better than do their pulse-based systems. I offer these users three recommendations.
The amount of oxygen delivered by a pulse system on each inhalation may be as little as 1/6 that of a continuous flow system at the same settings. For this, both oxygen providers and users are happy. Oxygen providers make fewer trips to deliver less oxygen to pulse system users and these users change or refill their portables less frequently.
To make pulse system this efficient, manufacturers of pulse systems use technology to improve the efficiency of oxygen delivery while trying to maintain its efficacy. Pulse systems sense when you begin to inhale and try to deliver as much oxygen as possible within the first several hundredths of a second. Some pulse systems stop oxygen deliver at that point whereas other systems continue delivery until exhalation is detected.
Manufacturers established the efficacy of their pulse systems through clinical studies whose subjects were oxygen users who were participating in rehab programs at the time. These subjects are typically on 2 Lpm prescriptions and have breathing rates of about 20 bpm. You should not be surprised if folks on a 2 Lpm prescriptions who have breathing rates of 20 bpm are ones who are more likely than not to set both their concentrators and pulse systems to the 2 setting.
Recently, a study was conducted to determine the effectiveness of pulse flow as compared with a continuous flow at different breathing rates and different settings. The study used several piece of equipment to emulate a human lung. Measurements were taken of the percent of oxygen that was in the air during each inhalation.
The following table shows the results of this study at three breathing rates.
Table 1
Oxygen concentration in simulated
lung at three breathing rates
(setting = 2)
The above table shows that average and fast breathers are likely to use the same settings on their concentrators and portable systems. The table also shows that slow breathers may not. Slow breathers may have prescriptions with pulse settings one or two positions higher than continuous flow settings.
The second comparison of the study is between different settings at the breathing rate of 20 bpm. The results are reported in the following table.
Table 2
Oxygen concentration in simulated
lung at three settings
(breathing rate = 20 bpm)
The implication of the above table is that 20 bpm users with 2 Lpm prescriptions will probably have the same continuous and pulse flow settings and that users with higher prescribed rates will not.
You can read the original study by going to Valley Inspired Products. The study was conducted by Peter Bliss and Bob McCoy of Valley Inspired Products and presented at AARC International Congress in 2000.
What should you glean from this discussion? There are some users whose prescriptions call for the different settings on concentrators and pulse flow systems. These differences may be related to breathing rate or to flow settings. It may be related to other factors not covered here.
In closing, let me paraphrase the recommendations from the above study, as follows:
© 2003 Copyright
Peter M. Wilson, Ph.D.
Founder of PortableOxygen.org
You have permission to print this document for your personal use. You also have permission to print, copy, and distribute this document to oxygen users and their caregivers.
Title and buttons courtesy of Ben Ledet, <email@example.com> Creative Director, Parker Medical, Englewood, CO. 80112


text:
SAN DIEGO (AP) - Two San Diego pit bull owners have been convicted in their dog's fatal mauling of a 75-year-old woman.
Alba Cornelio and her daughter 21-year-old Carla Cornelio were found guilty Monday of felony involuntary manslaughter and owning a mischievous animal that caused death.
The elder Cornelio cried in the courtroom after hearing the verdict and was removed by paramedics on a gurney.
In 2011, 75-year-old Emako Mendoza was in her backyard when the dogs entered through a gap in a shoddy fence the judge said the Cornelios should have mended.
Mendoza underwent amputations for her left arm and leg as a result of the attack, but died from severe infections and complications. She was 76 when she died.
They are due for sentencing March 11.
Copyright 2015 Associated Press. All rights reserved. This material may not be published, broadcast, rewritten, or redistributed.


text:
- Filed Under
The Monroe County department of health has confirmed a case of H1N1 flu, or swine flu, in a Churchville-Chili Central School District student.
However, doctors have not deemed the child contagious and the student has since returned to school.
The child, who attends Fairbanks Road Elementary School, also has siblings in the middle school and the Ninth Grade Academy. The student was treated by the family pediatrician and is feeling well, according to Amanda Wood, district spokesperson. ...


text:
- WND - http://www.wnd.com -
Egypt's Mubarak to be freed from jail
Posted By -NO AUTHOR- On 08/19/2013 @ 11:03 am In Front Page,Politics,World | No Comments
(FOX NEWS) Egyptian judicial officials have ordered former President Hosni Mubarak freed from jail, a stunning turnaround for the 85-year-old strongman who ruled the nation for three decades before being ousted in a popular revolution, and a move that could plunge the unraveling North African nation into further violence.
The announcement, which comes as Egypt is roiling with new protests following the July 3 ouster of Mubarak's successor, Mohammad Morsi, stoked fears of even more violent reprisals from the Muslim Brotherhood, whose supporters have clashed with security forces and torched dozens of Coptic churches. As many as 1,000 Egyptians, including 70 soldiers and police officers,have been killed in the last week in fighting between the Muslim Brotherhood and the nation's more secular Muslims and Christians. On Sunday, some 25 Egyptian police were ambushed and executed in the lawless Sinai Peninsula, where the Muslim Brotherhood appears to have aligned with Al Qaeda fighters.
Also on Sunday, 36 Islamists died as they were being transported to a prison outside Cairo. Government officials said they suffocated in the back of a prison van after tear gas was used on them as they rioted. The Muslim Brotherhood accused the interior ministry of killing the detainees "for their opposition to the bloody military council".
Article printed from WND: http://www.wnd.com
URL to article: http://www.wnd.com/2013/08/egypts-mubarak-to-be-freed-from-jail/
Click here to print.
© Copyright 1997-2013. All Rights Reserved. WND.com.


text:
Grade: B-
The rules of cinema dictate that if your film opens with lovers wallowing in one another's happiness, before the first reel is up one of them will be dead. So it goes with Delicacy, whose initial stretch depicts the beamingly wondrous life of young lovers Nathalie (Audrey Tautou) and François (Pio Marmaï) from meet-cute to early marriage. When François goes out for a casual run, it's no shock it winds up his last. Quite a bit less predictable is that, after three years and a handful of screen minutes of grieving, Nathalie will whimsically shove her tongue in the mouth of a slovenly stranger from Sweden.
We haven't seen Markus (François Damiens)—a hulking, balding, mouth-breathing, vaguely cloddish sad bachelor with over-prominent teeth, the type who ordinarily wouldn't even be in the supporting cast of an ostensibly cute Audrey Tautou movie—before the time he arrives in Nathalie's office, roughly 40 minutes in. His arrival, and his establishment as a permanent fixture in the narrative, is a good indication of Delicacy's agreeably restless nature, and the way it likes to playfully confound our expectations. We think we have the film, by brothers David and Stéphane Foenkinos (adapted from the former's bestseller), down pat—that it will be boilerplate bereavement porn—only to have it change focus and even protagonists. Delicacy begins in the head of François, lusting after Nathalie in a café, before shifting to her and then over to someone who wasn't even established until the film was well under way and into an altogether different groove.
That's not to say Delicacy reinvents the wheel; in fact the style is often mere window-dressing. The Foenkinos avoid some pat the-hottie-from-Amélie-dates-an-ugly-dude scenario, with Markus gradually revealing himself to be a charmingly aloof eccentric, played with oft-kilter timing by the Belgian Damiens. But they don't replace this void with anything that's particularly novel. It's not lacking in winning details, however: this may be the first movie that shows someone deleting their deceased spouse from their cell phone contacts. The same goes for a scene where Markus gets revved up for romantic pursuit by watching an (unsubtitled) Obama stump speech on TV. Delicacy is more likable than memorable, but likable will do.
Even once is too much for "Kill Me Three Times"
Blueblood entitlement's on the dinner menu in "The Riot Club"
Hawke delivers a quiet charmer in "Seymour: An Introduction"
"An Honest Liar" tackles truths, lies and consequences
Camera work in "'71" deserves same praise as its star
"She's Beautiful When She's Angry" a captivating look at activism
"A Girl Walks Home Alone at Night" a trippy, effective parable


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Iperf was developed by NLANR/DAST as a modern alternative for measuring maximum TCP and UDP bandwidth performance. Iperf allows the tuning of various parameters and UDP characteristics. Iperf reports bandwidth, delay jitter, datagram loss.
Latest News
JPerf 2.0.0 Released 2008-03-19 18:16 - Iperf
Nicolas Richasse has resurrected the jperf code base and brought it up to date. This is a binary
Read More »
Iperf 2.0.3 released 2008-03-18 21:41 - Iperf
Iperf 2.0.3 addresses several issues with Iperf. This release is a bug fix release and does not add any significant new functionality.
Bugs fixed in 2.0.3:
Read More »


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IBAN stands for International Bank Account Number. The IBAN facilitates the automation of cross-border payment transaction processing. Each country has its particular national IBAN format. The ISO 13616 standard specifies the structure of an ISO-compliant national IBAN format. A copy of the ISO 13616 standard can be obtained through http://www.iso.org/.
ISO has designated SWIFT to act as the registration authority for national IBAN formats. Only a national standards body or a national central bank can request a national IBAN format registration for its country. To request the registration of a national IBAN format or to update an existing one, download the IBAN Registration Form, complete it, and send it to firstname.lastname@example.com.
SWIFT publishes the ISO 13616 IBAN Registry. This registry contains the technical specification of the national IBAN formats of those countries that are compliant with the ISO 13616 standard. The IBAN Registry is updated upon request from the ISO national standards bodies or the national central banks. Download the IBAN Registry (in PDF format) free of charge. The Registry is also available in .txt format.
A number of organisations offer online tools to validate the structure of IBANs. SWIFT offers directory products specific to IBAN validation, more information is available from https://swiftref.swift.com/sepa-data.
In the scope of SEPA migration SWIFT offers its coprorate customers consulting services to prerpare and convert their domestic banking coordinates (BBANs) to IBAN (and BIC) format. For details and quotation please contact us on email@example.com.


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|Individual title rentals and subscription DVD rental plans from 2-8 DVDs at a time. All plans come with 60 free VOD minutes. 14 day free trial.
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|Watch now with pay-per-minute streaming video. Download or streaming movie rentals for 48 hours, 30 days or for life. Download to Own. 10 Minute Free Trial.
Christian Dark's review on 4/21/2010
read the movie review
Okay listen, Nat Turnher was in my eyes one of the weakest male performers in the game. his scenes always seemed to lack a certain amount of heat, it just did. I don't know what the hell happened but it seems as if Nat has found his love for the business and is putting out some really good movies as of late. When I seen Cherokee D'ass and Beauty Dior on the cover showing off those donkey asses I knew this was going to be one hell of a ride. Cherokee is featured twice here in another scenes with the super cute Melrose Foxx. Factor in what I'm calling the ass twins Mellanie Monroe and Austin Taylor, Marie Luv and shockingly Ms Jenaveve Jolie makes a special and shocking appearance here. Again the only problem I have here is that there is no BTS action. What's up with that. All this ass in this movie and no BTS!!! That's a bad thing, for a really excellent movie.


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Register with us or sign in
From 1 ratings
Plant type
Evergreen shrub
Flower colour
Scented flowers
Skill level
Although laurustinus comes from dry sunny areas around the Mediterranean, it has been cultivated successfully in northern gardens since the 16th century. It is now one of the most popular evergreen shrubs, as much for its luxuriant masses of glossy evergreen leaves, as for its long season of winter flowers. These first appear in October or November, and continue to open over a period of five months. It is a tough shrub in all but the coldest, most exposed gardens, and makes a perfect hedge in seaside areas. To propagate, take cuttings in summer. The Royal Horticultural Society has given it its prestigious Award of Garden Merit (AGM).
Family: Caprifoliaceae
Genus: Viburnum
Species: tinus
Cultivar: Gwenllian
Plant type: Evergreen shrub
Flower colour: White
Foliage colour: Dark green
Feature: Scented flowers
Sun exposure: Full sun, Partial shade, Shade
Soil: Well-drained/light, Dry
Hardiness: Hardy
Skill level: Beginner
Height: 300cm
Spread: 300cm
Time to take cuttings: June to August
execellant info, very explicit, happy to go out and buy one.


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As he so aptly noted, threats to the grid are real, the public should be made aware of the consequences, and we should "consider what we can do to harden our defenses – our electricity grid."
Although the segment focused on dangers posed by an electromagnetic pulse from a high-altitude nuclear weapon (HEMP) and solar flares, federal officials have warned that massive disruption caused by coordinated cyber attacks on the grid is not only possible, but merely a matter of time. Revelations about physical attacks on substations, domestically and overseas, have heightened awareness of the need for "all-hazards" grid security.
While experts say an extreme solar event will inevitably materialize, the use of a high-altitude nuclear EMP is heavily debated. It shouldn't be. It's not hard – a single weapon detonated at 275-300 miles above the general vicinity of Kansas City would remove the United States as an actor on the world stage instantaneously and long-term.
A 2008 National Academy of Sciences report estimated that recovery from an attack or solar event would take four to 10 years. Members of the Congressional EMP Commission estimated that two-thirds of the population would be dead within the first year. Other experts estimated losses as high as 90 percent.
Dr. Peter Vincent Pry, who served on the EMP Commission, offers this thought: "Pennsylvania is truly the 'Keystone State' for the Eastern Grid – indeed for the entire U.S., as Pennsylvania has more Extra-High-Voltage transformers [which are highly vulnerable] than any other state. Since 70 percent of U.S. electricity is generated in the Eastern Grid, America cannot survive without it."
As an officer in the Pennsylvania Army National Guard, Perry understands the nature of this threat. As a member of two relevant Homeland Security Subcommittees (on Cybersecurity & Infrastructure Protection and Emergency Preparedness, Response, & Communications) he is in a position to influence the content of legislation aimed at protecting the nation against catastrophic collapse of critical infrastructure.
In the context of this issue, he and his fellow congressional representatives may hold the fate of the nation in their hands. I sincerely thank Congressman Perry for being so bold as to tackle this enormously difficult problem.


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Venom Apache Helicopter
Sep 05, 2011 No Comments
This micro helicopter is ready for living-room combat! With a counter-rotating rotor design and built-in gyro, you will be able to easily navigate through those critical special ops assignments. With a charger conveniently built into the transmitter, you will always be ready to fly when duty calls. The rechargeable Li-Poly battery provides flight times of up to 10 minutes. It costs just $42.99, so you might as well buy two and pit your skills against an opponent!


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Solar Roofing Materials
Integrating solar cells into building materials could make solar power more attractive to homeowners.
In an effort to promote the adoption of solar technology, United Solar Ovonic of Auburn Hills, MI, has teamed with a major roofing company to create a metal roof system that generates electricity from sunlight. The partnership offers seven different prefabricated systems, ranging in capacity from 3 to 120 kilowatts. Tests show that the solar roof panels are rugged and can withstand winds in excess of 160 miles per hour.
In addition to being more aesthetically pleasing than bulky rooftop-mounted panels, solar roofing materials can cut the cost of household solar installations by doing double duty, generating electricity while protecting buildings from the elements. "Ultimately, if you can use one product to do two things, you can save a lot of money," says Cecile Warner, principal engineer at the National Renewable Energy Laboratory's National Center for Photovoltaics, in Golden, CO.
Building-integrated photovoltaics (BIPV) have been around since the late 1980s, Warner says, but only lately have they begun to see some success with large commercial and residential developments. Recent advances in flexible thin-film photovoltaic materials–such as those sold by United Solar–are allowing manufacturers to more easily integrate photovoltaics directly into the roofs and facades of buildings.
Nonetheless, many builders remain leery of the new technologies. "In the past, people in the construction industry have been burned by trying out new products," Warner says. In particular, she says, they're wary of products that would be difficult to recall should they prove defective. Roofing materials certainly meet that description. "I think that's probably been the sticking point all along," Warner says.
EnergyPeak, the partnership between United Solar and Pittsburgh-based Centria Services Group, is an attempt to allay this skepticism. "We worked with Centria to develop a program that would get our product out to a number of small installers because Centria already has the infrastructure to do this," says Marcelino Susas, vice president of strategic marketing at United Solar's parent company, Energy Conversion Devices, based in Rochester Hills, MI.
When solar companies partner with construction firms, "it gives the product a lot more credibility, and it helps to break down the barrier to adoption," says Warner.
Centria designs and assembles the solar roof systems using United Solar's adhesive thin films, which can simply be peeled off of their backings and stuck to the roofing materials. The company then distributes the final product through small metal-roofing manufacturers that do the installations for building owners and architects. EnergyPeak comes with a 20-year warranty and, depending on the state in which the solar roof is installed, could pay for itself in less than 10 years, Centria says.


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Speakers wow Housley Leadership students
Presidential adviser is part of presentation
SAN ANGELO, Texas - Students in Angelo State University's Housley Principled Leadership class got a lecture they will never forget Thursday, when three of Texas' most prominent leaders arrived to speak to them.
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Media News
Saturday, Oct 09
This Week in mb
Get On The Air: WPIX-TV New York
Hey, How'd You Establish Yourself as The Budget Fashionista, Kathryn Finney?
So What Do You Do, Justin Osofsky, Head of Media Partnerships for Facebook?
How To Pitch: Kiwi
Pitching An Agent: Felicia Eth Literary Representation
How To Pitch: Mother Jones
Video: Rick Sanchez: "Hold the Viewers' Attention, Get them on the Edge of their Seats"


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We've got 200 He-Shi Express Liquid to give away. Enter here between 3pm and 5pm on Friday 13th December for your chance to win.
BY Sonia Haria | 01 December 2013
Welcome to Stella Magazine's Big Beauty Giveaway. To celebrate the magic of beauty, we're giving away 14,000 of our favourite beauty products.
Every two hours between 9am and 7pm 200 of a particular product will be up for grabs.
Between 3pm and 5pm win one of 200 Express Liquid Tan by He-Shi (worth £7.95). This easy-to-use liquid self-tan gives you a summer worthy glow.
Find out which other amazing beauty products are up for grabs in the STELLA BIG BEAUTY GIVEAWAY


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OKOLONA – James Toliver Carter, 93, died Monday, March 4, 2013, at Trace Regional Hospital in Houston. He was born April 9, 1919, in Woodland to James Carter and Mary Martin Carter.
As a lifelong resident of Okolona, he attended school there and worked many years in general maintenance for the City of Okolona before retiring in 1976. He was a hard worker, enjoyed his chickens and his yard. He frequently and greatly enjoyed sitting on the front porch of his home with friends and neighbors. He was of the Baptist faith.
A memorial service celebrating his life will be at 11 a.m. Thursday in Okolona Chapel of Holland Funeral Directors with Bro. Jimmy Bryan officiating. Burial is private. Visitation will be from 10 a.m. to service time only. Holland Funeral Directors Okolona Chapel is entrusted with arrangements.
Survivors include his son, James Wayne Carter (Diane) of Okolona; two daughters, Virginia Mangus of Pickwick Lake, Tenn., and Marty Anderson of Pasadena, Texas; nine grandchildren; 21 great-grandchildren; and a host of nieces and nephews.
He was preceded in death by his parents, two brothers, two sisters, and a son, Allen Carter.
A complete obituary will be published in the Wednesday, March 13, Chickasaw Journal.
Condolences may be emailed to firstname.lastname@example.com.


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Capstone Project
As a directed study course, the capstone course requirement is a tangible project, often work or community related. As the culminating experience in the BID curriculum, it is taken during a student's last semester or two in the program; it demonstrates the synthesis of academic contact with personal and professional goals. Students can earn up to 12 undergraduate credit hours over two semesters.
Capstone Goals/Process
- Student and advisor and a project director agree on a project.
- Student submits proposal to director and advisor early in the semester prior to when actual project begins.
- Directing Professor recommends changes or requirements for the project, e.g., literature searches, expert consultants, timetable, etc.
- Draft of the final report due to director and advisor by the student delineates the following:
- Goal or outcome of the project
- Credit hours and number of semesters involved
- Biweekly telegraph style reports are due to advisor
- Mid-term report expanding on biweekly reports and incorporating any positive or negative progress of the project. Comments on short and long term goals or a SWOT analysis of the progress
- Draft of final report due to advisor at least 10 days prior to the end of the semester or earlier to allow time for suggestions and revision.
- Final report or preface to the project itself discusses and documents how the project has integrated the four competencies of the on-line BID. The final report should, as much as possible, share how these competencies have expanded over the course of the semester or the project.
- For
- final capstone project is stated (portfolio, PowerPoint presentation, web pages, paper, CD, brochure, video, etc.)
- Capstone signoff sheet must be included which states if permission is granted to use for educational purpose
Sample Capstone Projects
- City tax to support the library will document the trials and tribulations of an initiative to have formal support for maintaining the library. This 12 hour project spread over three semesters will document all the issues that the library director faces in order to get a proposal on the ballot. The last component will be formalized such that everything will be placed onto a CD ROM or a series of Web pages.
- Another student is going to document how her role as president of a Chamber of Commerce necessitates all aspects of the goals of the degree. As this one is still in its developmental stages, its final outcome is yet to be determined.
- Physical aspects of youth recreational activities is a capstone project also in the developmental stages between the student and the advisor. However, this project is not work related as are the prior two, but a parental interest by the student who happens to work as an LPN.
- Through discussion, a student discovered his job responsibilities required phone and email communication with people all over the world. This potential capstone will focus on multicultural aspects of his duties, and a possible development of a handbook for other employees who need to do the same type of communication.
- A student interested in computer science is going to develop a set of protocols for running a computer lab. This will entail not only the implementation of the Lynix based operating system but also the guidelines for the help desk and user regulations. This, as the others, will integrate the four goals of the program.


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San Francisco 49ers Social Media Playbook Includes Profitability - Posted May 23, 2013
On April Fool's Day 2013, San Francisco 49ers social media manager Scott Kegley decided to have a little fun at the expense of coach Jim Har... [FishbowlLA]


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Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF.
This is meant only for single-sample analysis. To analyze multiple samples, see the Best Practices documentation on joint analysis.
If you do not specify these parameters yourself, the program will use default values. However we recommend that you set them explicitly because it will help you understand how the results are bounded and how you can modify the program's behavior.
This specifies how we want the program to determine the alternate alleles to use for genotyping. In the default
DISCOVERY mode, the program will choose the most likely alleles out of those it sees in the data. In
GENOTYPE_GIVEN_ALLELES mode, the program will only use the alleles passed in from a VCF file (using the
-alleles argument). This is useful if you just want to determine if a sample has a specific genotype of interest and you are not interested in other alleles.
This is the minimum confidence threshold (phred-scaled) at which the program should emit sites that appear to be possibly variant.
This is the minimum confidence threshold (phred-scaled) at which the program should emit variant sites as called. If a site's associated genotype has a confidence score lower than the calling threshold, the program will emit the site as filtered and will annotate it as LowQual. This threshold separates high confidence calls from low confidence calls.
The terms called and filtered are tricky because they can mean different things depending on context. In ordinary language, people often say a site was called if it was emitted as variant. But in the GATK's technical language, saying a site was called means that that site passed the confidence threshold test. For filtered, it's even more confusing, because in ordinary language, when people say that sites were filtered, they usually mean that those sites successfully passed a filtering test. However, in the GATK's technical language, the same phrase (saying that sites were filtered) means that those sites failed the filtering test. In effect, it means that those would be filtered out if the filter was used to actually remove low-confidence calls from the callset, instead of just tagging them. In both cases, both usages are valid depending on the point of view of the person who is reporting the results. So it's always important to check what is the context when interpreting results that include these terms.
Run the following GATK command:
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R reference.fa \
-I preprocessed_reads.bam \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o raw_variants.vcf
Note: This is an example command. Please look up what the arguments do and see if they fit your analysis before copying this. To see how the -L argument works, you can refer here: http://gatkforums.broadinstitute.org/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals#latest
This creates a VCF file called
raw_variants.vcf, containing all the sites that the HaplotypeCaller evaluated to be potentially variant. Note that this file contains both SNPs and Indels.
Although you now have a nice fresh set of variant calls, the variant discovery stage is not over. The distinctions made by the caller itself between low-confidence calls and the rest is very primitive, and should not be taken as a definitive guide for filtering. The GATK callers are designed to be very lenient in calling variants, so it is extremely important to apply one of the recommended filtering methods (variant recalibration or hard-filtering), in order to move on to downstream analyses with the highest-quality call set possible.
Geraldine Van der Auwera, PhD
I am trying to revisit the documents for HyplotypeCaller.
I found a webpage seems also taking about HyplotypeCaller: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html
which one is the one to follow: this one or the one I copied and pasted here above? Since there are some difference between these two documents: e.g., one has --genotyping_mode DISCOVERY and the other does not have.
This page seems a new one for HaplotypeCaller, I used to use --enable_experimental_downsampling -dcov 10, -minPruning 10 etc, are those options still working? I check the command with -h, minPruning seems still there, but not --enable_experimental_downsampling. And also I noticed that -I reduced_reads.bam as input in this document, does that mean I need first run ReduceReads as mentioned in the following URL?
ReduceReads is equivalent of --enable_experimental_downsampling option?
Thanks a lot for your help!
Hi Mike,
These are two different kinds of pages.
The http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html page is the technical document that describes the capabilities of the tool and all its possible options. The command line shown there is just a general usage example, it does not represent THE best way to use it.
This page here is a tutorial that explains at the beginner level what are the important options and what they mean. For processes that involves several steps, like BQSR, the tutorial explains how to run the tools in succession. The tutorial (howto) pages do not include advanced options, but those options are still available for users who know of them and know how to use them.
--enable_experimental_downsampling option is gone since version 2.4 (or 2.5 maybe?) because the then-experimental downsampler replaced the previous downsampler. So there is no longer any reason to specify which downsampler to use. The default one is the new and improved one.
Finally, ReduceReads is an additional processing step that compresses your data. It is quite different from downsampling. It is optional, so you don't have to use it. The input file here is named like that because this content was extracted from another document that contained all the steps. I will change the name to avoid any further confusion.
Geraldine Van der Auwera, PhD
Dear Geraldine:
Thanks so much for your comments and info, which are very helpful!
Last time I run HyplotyperCaller, it runs forever and I started to use option -minPruning, which finally works in speed for my old dataset until version 2.2.4 or 2.3-9-ge5ebf34 so that I can finish it in reasonable time frame. For the new version 2.6-4, is it still necesssary to use this option? Of curse it may depend upon dataset, I just wonder about general guidance here.
still kind of confused about the genotyping_mode DISCOVERY, not sure the difference DISCOVERY vs GENOTYPE_GIVEN_ALLELES etc. Is it good for finding the rare-allelic variant?
Thanks again for your great help!
Hi Mike,
HaplotypeCaller gets faster with every release, but you may still need to use
-minPruning with version 2.6. Best thing to do is try it both ways and see how it goes.
As explained elsewhere, GENOTYPE_GIVEN_ALLELES mode is meant for when you know the alleles you are looking for. Let's say you are a clinician, you have patients with a genetic disease, and you know that usually this disease is caused by a specific mutated allele of a known gene. If you have your patients' exome data, you can very rapidly run in GENOTYPE_GIVEN_ALLELES mode to find out whether your patients have that allele or not. Or if there is a set of candidate genes with known disease-causing alleles, you can use the same thing to find out which of the alleles your patients have. You're not trying to discover something new, you're trying to identify something that is known. Make sense?
Geraldine Van der Auwera, PhD
Thx so much for your info, Appreciated very much as usual! Mike
I have been running the nightly version of GATK (due to an error in ReduceReads stage). I am now using the following HaplotypeCaller command to call variants:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -I reduced_reads_1.bam --dbsnp dbsnp_137.b37.vcf --genotyping_mode DISCOVERY --output_mode EMIT_VARIANTS_ONLY --stand_emit_conf 10 --stand_call_conf 30 -o raw_variants_1.vcf
With the GATK version nightly-2013-07-16-g515d8e5, I have the following error message:
With the GATK version 2.6-4-g3e5ff60, I have a similar but different error message:
Thank you for your help on this.
Hi there,
I'm not sure what's going on with the
output_mode argument, but for the other one the issue is that there was a typo in the tutorial. The argument was given with two dashes instead of one. I fixed it now.
Geraldine Van der Auwera, PhD
Addendum: the error you're seeing with the
output_mode argument is because that argument has been removed in our development version (which will eventually be released as version 2.7), and that functionality has been replaced by another argument,
--emitRefConfidence (or
-ERC for short). This gives you the option to get reference confidence scores for non-variant sites. It is a new experimental feature and we're interested in feedback about it, so you are welcome to try it out. For more details, see the announcement here: http://gatkforums.broadinstitute.org/discussion/2940/reference-confidence-calculation-gvcf-available-in-haplotypecaller-in-gatk-2-7
Geraldine Van der Auwera, PhD
Hi Geraldine,
Just a simple question about the –stand_emit_conf and –stand_call_conf.
Say I want to chose –stand_call_conf as 20 and –stand_emit_conf as 10.
I know that anything below –stand_emit_conf will be removed entirely and anything above 20 will be considered a high confidence call.
Now would calls with quality scores between 10 and 20 be considered low confidence calls?
Thank you
Yes, that is correct.
Geraldine Van der Auwera, PhD
Dear Geraldine, I had hoped I wouldn't have to ask your advice so soon already, but I've run into an issue with the haplotypecaller (you recently gave me some very valuable feedback on RG, indel realignment and base recalibration!). My question about the haplotypecaller concerns the multithreading. On the website (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html) it says that the program can be run in multi-threaded mode using -nct. I've tried this using just 5 samples (i.e. input 5 bam files) and I see the following line in the output: "MicroScheduler - Running the GATK in parallel mode with 24 total threads, 1 CPU thread(s) for each of 24 data thread(s), of 64 processors available on this machine". The program runs fine, but it won't use more CPUs than when I run it without the -nct option. When I click on the link of the –nct option on the website, it goes to the option to specify number of threads with -nt, but when trying this I get an error message that the haplotypecaller does not support multi-threading. So now I'm a little confused:) I hope there is a solution, because the analysis is very slow this way. Especially for the base recalibration I have to call SNPs on all my 40 genomes at once (to make the SNP reference file), which might become too impractical with this speed. Many thanks! Sanne
Hi @sanne,
Don't worry, there is no formal quota to the number of questions you can ask per period of time
I see what you mean regarding the link; actually it is taking you to the correct option (-nct), but due to a quirk in the website layout, that option is hidden by the black bar at the top of the screen, and you just see the -nt option a few lines below. If you scroll a little upward after clicking the link you will see it. I need to fix that in the website code.
Regarding what you're seeing, let me consult with one of our software engineers on whether this is the expected behavior or not.
Geraldine Van der Auwera, PhD
@sanne, can you tell me how you are checking how many cores are in use when you run this? Are you using top (table of processes) or something else?
Geraldine Van der Auwera, PhD
@Geraldine, yes I'm using top. And the expected run time of the program (checked after approx 30 min) is not very different whether I run with -nct 3 or -nct 24 or without -nct option specified.
@Geraldine, sorry I should be more specific - the estimated run time when running with -nct 24 was twice what it took with -nct 3 (9 versus 4.5 days). The only other setting I changed was -stand_call_conf and -stand_emit_conf, which were set to 30 in the run with -nct 24, and to 4.0 in the run with -nct 3.
Oh, I see. Well, the confidence threshold shouldn't have any effect on runtime. As for the time differences that you're seeing, it's difficult to comment on. Using the estimated runtime as proxy can be problematic, especially for a big job, and after a relatively short time of actual running. It may be that the extra start-up overhead involved by the high level of parallelization you requested with -nct 24 skewed the estimate significantly. It would be more informative to evaluate actual runtimes, or (considering you may not want to let something run for a week before making a decision) evaluate the estimated runtimes after at least several hours or actual run.
Geraldine Van der Auwera, PhD
Hi Geraldine, the 4.5 days was actual run time, the 9 days was the estimate it gave me after 3 days of running. However, I killed that run yesterday and started it again, and this time it only took 20 hours! I gave it the exact same command, so it seems something just went wrong in the one before. So sorry to have bothered you with this false alarm! But I am very happy now that I know I can just go ahead and do more runs without it taking weeks Cheers!
hi, Geraldine,
If the input files include multiple sample bam files, are the QUAL, FILTER, and INFO of the output vcf file computed using the pooled aligned reads from all samples? how is the genotyping different from running HC with just one sample bam file?
Between running HC with all samples of a cohort together and running HC with each sample separately, is it possible the genotyping results are different for some samples? If so, when could that happen?
Hi @blueskypy,
When you do multisample calling, the fields that refer to the variant site itself, such as QUAL, FILTER, and INFO, are all computed based on pooled reads from all samples, yes. The HC's variant calling process (which is not the same thing as genotyping, strictly speaking) starts with a local de novo assembly step that uses all the reads, regardless of what sample they come from, so it is quite different from running HC on bam files individually. This can indeed lead to genotype calls that are different for samples that are run individually vs. with others. The reason is that when you use reads from all the samples, you can end up resolving that big pile of reads into different haplotypes than if you were just using the reads from a single sample. This is normally a good thing because if you are processing a cohort of samples, there is a population effect that compensates for potentially poor sequencing that might affect some of the individuals. But if you're processing wildly different samples together that can potentially confuse the assembly process, so it's important to only process samples together if they form a cohort that makes sense.
Geraldine Van der Auwera, PhD
hi, Geraldine,
Thanks for your explanation! I agree with you totally! However, my boss just does not like the idea that the genotying result of a sample may depend on the composition of the cohort, and thinks that each sample should run with HC separately. So I wonder if you can recommend any docs or papers that illustrate the benefit of calling all the samples of a cohort together vs separately?
I'm not aware of any papers that have done this comparison in detail, but if you look at the 1000 Genomes publications, all that was done with multisample calling. Note that now if you have decent quality sequencing data, any differences should be minimal. The problem with single-sample calling is that you won't be able to perform variant recalibration, and will be stuck with hard filtering, which is an inferior method.
Geraldine Van der Auwera, PhD
Dear Geraldine,
I am experiencing strange errors with the command adapted from above.
The whole workflow until this point worked like a charm (thanks for your great pages with code, this is really the way to go for me)
The env variables are ok as they were used until this point already. I use a freshly installed GATK.
Any idea what could be wrong?
Thanks and cheers from BE.
java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \
> -T HaplotypeCaller \
> -R ${reference} \
> -I ${result}/reduced_reads.bam \
> -L chr21 \
> --genotyping_mode DISCOVERY \
> --output_mode EMIT_VARIANTS_ONLY \
> -stand_emit_conf 10 \
> -stand_call_conf 30 \
> -o ${result}/raw_variants.vcf
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR MESSAGE: Argument with name 'output_mode' isn't defined.
Hi @splaisan,
Actually this is my bad; the output_mode argument was deprecated in 2.7 and I forgot to update the tutorial. I will fix that asap, thanks for pointing it out.
Geraldine Van der Auwera, PhD
I removed the guilty parameter and it worked. I will see later if a replacing argument comes to shine.
Does HaplotypeCaller fully support ReduceReads bam files now? I read an old post about this where caution was suggested for this at the time under dev application (just to make sure I am not doing some mistake!).
Thanks again for the great DOC!
Hi Stephane,
For HC, by default it will only emit variants, and there is no replacing argument as such, but there is a different argument that now allows you to emit reference calls with confidence scores. Have a look at this document:
HC now handles reduced bams just fine, yes. If that caution note is in one of our docs (as opposed to a user's question/discussion thread) let me know and I will update it.
Geraldine Van der Auwera, PhD
This new argument recalls me of Complete Genomics calling ref positions which is extremely useful when comparing several genomes with one having a variant and often not knowing if others were ref or just not-sequenced at this given position. Thanks for pointing to that page.
When calling variants on a full genome scale, is it correct to split the calling based on the same full bam file over 22+ parallel jobs using the L parameter or should I call against the full target genome in a single run?
I fear that the first approach will ignore the important information for those reads mapping alternatively to several possible chromosomes and bias the calls towards the -L chosen target.
What is the best practice for parallelization of the calling step using HaplotypeCaller?
Calling based on the same full bam file over 22+ parallel jobs using the -L parameter is absolutely fine. GATK ignores alternate mappings anyway; it will only consider primary alignments.
Geraldine Van der Auwera, PhD
Hello Geraldine,
I was doing pretty well so far following instructions in Best Practices and troubleshooting the occassional hitch, but I now have a problem I am not sure how to tackle. I tried to use HaplotypeCaller to call variants in a preprocessed BAM file that I generated from a fastq file of a single patient's exome using the guidelines in best practices. I used the parameters recommended in Best Practices, and obtained an output file with around 1.1 million variants. I then ran the VariantFiltration tool on snps, again with the recommended parameters, hoping that I would end up with a more reasonable number of variants. But I still had ~900,000 snps that passed the filter, which can't be right. I repeated the variant calling process with UnifiedGenotyper just to see if there was a difference but I ended up with similar numbers. I am wondering if there is something wrong with my bam file (This is my first ever experience with handling raw exome data)? Any suggestions/comments will be much appreciated. Below is the command I used for HaplotypeCaller
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R '/home/megana/Desktop/Sequence_Analysis_Tools/GATK_Tools/resource_bundle/human_g1k_v37.fasta' -I '/home/megana/Desktop/HDS_05/reduced_HDS_05_5.bam' --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o raw_variants_HDS_05_5.vcf
Running the VariantFiltration with the following command
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R '/home/megana/Desktop/Sequence_Analysis_Tools/GATK_Tools/resource_bundle/human_g1k_v37.fasta' -V '/home/megana/Desktop/HDS_05/raw_snps_HDS-05_5.vcf' --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0" --filtername "GATKbestpractices" -o '/home/megana/Desktop/HDS_05/filtered_snps_HDS-05_5.vcf'
led to several warnings such as
WARN 14:25:11,496 Interpreter - ![63,84]: 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0;' undefined variable MappingQualityRankSum
but based on another thread I don't think this is a problem.
Thank you for your help and for the wonderful tool/resources the team has made available to the community.
Hi Megana,
You should try calling your variants with an intervals file corresponding to the exome capture targets of your experiment (use the -L argument). This will restrict the analysis to only the targeted exons and should eliminate variants called in off-target regions. See if that helps...
Geraldine Van der Auwera, PhD
Hi Geraldine,
That worked like a charm- I now have ~44,000 variants. Thanks for the prompt response!
@Geraldine_VdAuwera said:
I'm not aware of any papers that have done this comparison in detail, but if you look at the 1000 Genomes publications, all that was done with multisample calling. Note that now if you have decent quality sequencing data, any differences should be minimal. The problem with single-sample calling is that you won't be able to perform variant recalibration, and will be stuck with hard filtering, which is an inferior method.
Hi @Geraldine_VdAuwera, could you kindly explain a little bit more why HaplotypeCaller on single sample could not be followed by VariantRecalibrator? I didn't found related info in other places.
EDIT: I found in FAQ section...
Hi Geraldine,
I was wondering if you can kindly provide some insight regarding the effect of the number of input samples passed to HaplotypeCaller. My first question is, is there any quantitative way of thinking about how much of a benefit one gets from passing 5 samples as opposed to doing it on a single BAM file? My second question is sort of along the same lines. In a scenario where one is restricted to a single patient data for variant calling. Would passing multiple normal tissue samples from the same individual to HaplotypeCaller improve performance, or would it be axiomatically wrong? My naive thought is that the same variant appearing across multiple samples should provide a stronger signal, but this setting could also lead to introduction of confounding factors (population structure) not accounted for by the model.
Thanks a lot!
Hi Geraldine,
I'm just wondering whether it would be appropriate to reduce the value of the --maxNumHaplotypesInPopulation parameter when calling one diploid sample at a time? E.g., would it be reasonable to set this parameter to 2?
(I'm working on an extremely diverse species and evaluating HaplotypeCaller in GVCF mode and looking for ways to reduce runtime.)
Hi @noushin6,
There is indeed; it's a matter of likelihoods. If you have a potential variant call in a single sample but it's not well supported (low alleleic fraction etc) the likelihood is high that it's just an error. But if you see the same thing in another sample, it's less likely to be an error and more likely to be real. This can be formalized using Bayesian probabilities.
I'm not sure what the effect would be of passing multiple samples from the same individual as if they were a population. I think you'd be better off grouping the data and analyzing it together as different libraries of the same individual. This should help resolve any issues that are due to sequencing errors and/or low coverage, which are some of the most frequent causes of calling difficulties, by boosting signal in a way that doesn't introduce other potential issues.
Geraldine Van der Auwera, PhD
Thanks so much for the prompt response, and all that useful information.
Just to make sure I get it right, in a situation that one is stuck with one individual, you suggest that it is best to merge the bam files corresponding to multiple samples of same individual into a single file with multiple libraries, and pass it a s a single input to HaplotypeCaller. Please let me know if this is incorrect.
Hi Alistair, How are you?
That parameter is a convenient upper limit to avoid falling into CPU sucking traps, seemly complex regions that result very complex local assemblies with far too many possible haplotypes.
Anyone is welcome to change the default 128 to something smaller, say 64 or 32 whatever one considers reasonable.
Now, if you have a single diploid sample the biology is that it only should have 2 true haplotypes, yet this does not necessarily means that the assembly would just reconstruct two haplotypes even with perfect data (mapping and sequencing error free).
For example if you have 2 balletic variants that are distant enough, more than a kmerSize (10 and 25bp by default), all the 4 possible haplotypes are likely to be generated by assembly and you actually want them to progress down to genotyping.
There is not a straight answer to what should be the minimum but based on the restriction aforementioned if you expect to analyze regions with up to X variant clusters (form by contiguous variant sites no further than 10, 25bp of each other) you would need --maxNumHaplotypesInPopulation to be at the very least 2^X.
@valentin Hi Valentin, good to hear from you, hope you're enjoying life in Boston! I'm good thanks, currently wrestling with a deluge of Anopheles data :-)
Thanks a lot for your answer, this is really helpful. I must admit my understanding of the HaplotypeCaller is still very sketchy, is there any technical documentation or slides on HaplotypeCaller internals that I could read (before I ask a lot of dumb questions)?
Just to give you the full background, we're trying to call variants across ~1400 Anopheles gambiae samples, hitting scalability issues with UnifiedGenotyper, hence the interest in the HaplotypeCaller and gVCF. Based on earlier calling runs with UnifiedGenotyper on fewer samples, we're expecting SNP heterozygosity in the range 0.02-0.04 over most of the genome. So that's a het genotype every 25-50bp on average. We're going to do an evaluation of the HaplotypeCaller some time in the next couple of months, hoping that gVCF and the new approach for multi-sample calling will solve some scalability issues. However I know from some very limited runs of HaplotypeCaller on A. gambiae samples that it is much slower than Unified Genotyper. Hence I'm looking for any tips or tricks that might reduce runtime when running HaplotypeCaller one sample at a time. And I'm also trying to figure out what might happen when HaplotypeCaller runs on on samples with high heterozygosity.
@aliman We're working on an HC doc article (with Valentin's help) right now -- should have something ready to share with the public in another week or so.
Geraldine Van der Auwera, PhD
@noushin6 Yes, if I understand your experimental design correctly, and they're not cancer samples -- right? If they're cancer samples then that's probably not the right thing to do. But normals should be fine to merge.
Geraldine Van der Auwera, PhD
@aliman Live in Boston is treating me good thank you. Hopefully that techdoc would suffice otherwise you are welcome to ask details and we can improve it even further.
In recent times the group has worked into getting GATK to run faster using specialized hardware (e.g. GPU, you have access to those?) and alternative faster ways to calculate likelihoods. So is posed to improve overtime.
Also if most sample seem to get stuck in particular regions of the genome, for example due to a poor reference sequence, you could analyze them separately. So for the "easy" portion of the genome you could use a faster setup.
What kind of times are you getting with UG and HC?
In any case more variation means more number churning thus more CPU time so the more distant from the reference the longer it will take.
Thanks so much @Geraldine_VdAuwera !
Hi Geraldine,
I saw your announcement "Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix."
In this announcement, please let me know what command produce this bug.
@knho It happens whenever you specify an output vcf filename that ends with
Geraldine Van der Auwera, PhD
@aliman said:
Hence I'm looking for any tips or tricks that might reduce runtime when running HaplotypeCaller one sample at a time.
Yes I am in a similar situation with 550 cattle. i have done a parameter sweep on the -max_alternate_alleles and maxNumHaplotypesInPopulation paparemeters. Initial results were encouraging. They were only over a very small potentially non representative region for a single high coverage animal. My thoughts were that you need to consider at least three haplotypes :two for the sample and one for the "reference" haplotype. I am quite keen to learn anyone elses experience before I fire off haplotype caller on the whole population!
@MikeK You'll want to give HC more elbow room than that, for two reasons.
At the single-site level: if you force HC to consider only "ploidy+ref", you limit its ability to store information about other alleles, which may be of interest if the allelic ratios are not clear-cut. If you allow it to consider more possibilities, this information will be recorded in the GVCF and may make a difference in the joint genotyping step (assuming you're following our new best practices pipeline, which you really should).
At the level of the entire active region: any given active region that the HC may contain more than one potential variant sites. If that is the case, HC needs to consider all possible haplotypes representing the different combinations of variants, especially if the physical phasing is not obvious. So be really careful when you constrain the number of alt alleles and max haplotypes as this can severely handicap the HC's ability to do its job.
Geraldine Van der Auwera, PhD
Hi,there! Recently I used HaplotypeCaller to detect SNP and indels according to the best practice. Unexpectedly, some large indels (up to 200bp) were reported. I remember that HC can detect indels of up to half the length of the read. I wonder if this is normal? Here is my command:
for generating gvcf files:
java -jar GenomeAnalysisTK.jar
-R galgal4.fa
-T HaplotypeCaller
-I sample.recal.bam
-o sample.g.vcf
-log sample.haplotypecaller.log
-D /home/Data/Temp2/INDEL/New2/dbSNP.vcf
--min_base_quality_score 20
--min_mapping_quality_score 20
--emitRefConfidence GVCF
--variant_index_type LINEAR
--variant_index_parameter 128000
-nct 20
java -jar GenomeAnalysisTK.jar
-R galgal4.fa
-T GenotypeGVCFs
-V sample1.gvcf
-V sample2.gvcf
-o all.sample.vcf
-log sample.genotypegvcfs.log
-nt 3
Hi @Jack,
The HaplotypeCaller is now capable of calling indels larger than the read size. In practice the size of indels it can call is mainly limited by the maximum size allowed for ActiveRegions, which can be customized. So your results are not a cause for concern.
Geraldine Van der Auwera, PhD
Thanks, @Geraldine! Your answer are always so timely !
I am running for the first time variant calling on one sample. Used the following command provided in this thread.
For the input file used (reduced_reads.bam ~150G) generated from the step - recalibration to your sequence data.
Do we need to Compress the reduced_reads.bam file before running the variant caller command?
It looks like it is going to take really long time ~50 hrs to run this for 1 sample.
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R reference.fa \
-I preprocessed_reads.bam \ # can be reduced or not
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o raw_variants.vcf
Also, when I ran the variant caller the output says sample1. Is there a way one can change the sampleID?
Hi @Usha,
We no longer recommend compressing data with ReduceReads -- in fact the tool is no longer included in recent versions of GATK. You should run the variant calling command directly. Be sure to read the Best Practices section of the Guide for details on the proper workflow to follow.
To change sample identifiers, you will need to use the Picard tool AddOrReplaceReadGroups.
Geraldine Van der Auwera, PhD
Hi there,
I am developing a workflow for SNP-calling for the first time and I have a few questions about the joint genotyping protocol vs. directly call the variant sites for my samples altogether. We work with a non-model organism so we are using a reference genome about 20 million years divergent, and we have around 600 samples sequenced through GBS. My questions are:
Thanks for your attention!
1) What exactly is your end goal? Although your reference is very divergent from your samples, do you expect your samples to all have the same variants?
2) To filter your variants to create a highly confident callset, you can use hard filtering. Have a look at this article for some help: http://gatkforums.broadinstitute.org/discussion/2806/howto-apply-hard-filters-to-a-call-set Please note, you may have to adjust some of the thresholds to better suit your callset.
3) The GVCF workflow is not only better for adding samples later on, but also better for scalability. With 600 samples, it will be faster to use the GVCF workflow.
Hi Sheila, thanks for such a quick answer. Our goal is to reconstruct the phylogeny of a recently diversified group of passerines and perform genome scans to check for regions under selection. So I'm not interested in variants in my samples with respect to the reference genome (the zebra finch) but among them, which I understand that are called during the joint genotyping step when using the GVCF workflow, am I right ? any comment or specific option to set in this regard? Thanks a lot!
Hi Guillermo,
Yes, the GVCF workflow will give you the variants in your samples with respect to the reference. However, you can use SelectVariants to find the variants that are the same and different between your samples. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php
Hi Sheila,
How exactly should I use the SelectVariant tool? This commands would be right, by passing a list of names fto the -sn argument?
"java -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T SelectVariants \
-R reference.fasta \
-V input.vcf \
-o output.vcf \
-sn SAMPLE_1_ACTG \
-env \
On the other hand, I'm not sure of the behavior of SelectVariants when there are heterozygous at reference-relative variant positions, can a variant heterozigous site between my samples be filter out because both of the samples have an alternate allele matching the reference?
Many thanks once again
Hi Guillermo,
There are a few different ways to go about using SelectVariants. It depends on what you are looking for. Would you like to find sites where your samples all have the same alternate allele? Or, do you want to find sites where your samples not only have the same alternate allele, but also the exact same genotypes? Or, are you interested in simply finding sites where all your samples have some alternate allele, even if the alternate allele is not the same for all samples?
Hi Sheila,
I think the last option would be the most fitting. I assume that with alternate allele you mean the lower frequency allele. For sake of clarity, I'm interested in any kind of among-sample variant within my set of samples, since they are intended to phylogenomics and population genomics analyses. There are going to be a lot of variants with respect to the reference shared by all my samples (this is, different from the reference but invariant within my sample set), since my reference genome is something like 20M years divergent. This positions I'd like to remove from my final .vcf file, since they are not informative for my purposes. I hope I explained myself clearly.
Thanks a lot.
Hi Guillermo,
Sorry for the late response. First, when I refer to alternate allele, I mean the allele(s) that are not reference. The alternate allele does not necessarily have to be the lower frequency allele.
I think you are trying to get the sites where the alternate allele is different for the samples in your dataset. So, you will be restricting your analysis to multi-allelic sites. You can get those sites with SelectVariants and restrictAllelesTo MULTIALLELIC. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php#--restrictAllelesTo
I hope this helps.
P.S. After you get the multiallelic sites, you can use the JEXL expressions to determine which samples are heterozygous and homozygous variant for each allele. https://www.broadinstitute.org/gatk/guide/article?id=1255


text:
|Influence of unsaturated carbonic acids on hemocompatibility and cytotoxicity of poly-vinylacetate based co-polymers.
MedLine Citation:
|PMID: 20162328 Owner: NLM Status: MEDLINE
|The aim of this study was to investigate hemocompatibility and cytotoxicity properties of synthetic polymer coatings containing various unsaturated carbonic acids with vinylacetate. Co-polymers of vinylacetate and crotonic acid (CA), maleic acid (MA), and itaconic acid (IA) were made. The materials were characterized in terms of their adhesion to metal supports (titanium and stainless steel) as well as hemocompatibility (% hemolysis, wettability, erythrocyte aggregation, hemoglobin content, thrombocyte count and lipid peroxidation levels) and cytotoxicity (human endothelial cell activity in vitro and chromosome aberrations, bone marrow proliferation and cell ploidy in rats). Co-polymers of unsaturated carbonic acids with vinylacetate exhibited good hemocompatibility properties, as opposed to vinylacetate homopolymer for which substantial levels of hemolysis were observed. By coating the metal supports with co-polymers the cytotoxic effects associated with the bare metal samples were markedly reduced. MA samples showed excellent hemocompatibility and no cytotoxicity, yet they lacked good adhesion properties to metal substrate, probably due to high water content. CA samples, having the highest density of carboxylic groups among the samples under investigation, showed increased bone marrow proliferation activity and cell ploidy in rats, as compared to controls. The most promising results in the present study were obtained for the samples with IA, which showed good adhesion to metal substrates, good hemocompatibility and low cytotoxicity. Thus, co-polymers of vinylacetate and IA rich in carboxylic groups are promising materials for the design of novel drug-eluting stents.
|N B Tavakalyan; A G Karapetyan; A S Pogosyan; A K Abrahamyan; A Corti; A Pompella; A Mihranyan
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Publication Detail:
|Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-02-17
Journal Detail:
|Title: Journal of materials science. Materials in medicine Volume: 21 ISSN: 1573-4838 ISO Abbreviation: J Mater Sci Mater Med Publication Date: 2010 May
Date Detail:
|Created Date: 2010-05-12 Completed Date: 2010-09-10 Revised Date: -
Medline Journal Info:
|Nlm Unique ID: 9013087 Medline TA: J Mater Sci Mater Med Country: United States
Other Details:
|Languages: eng Pagination: 1693-702 Citation Subset: IM
|Yerevan Institute Plastpolymer, Arshakunyats Ave. 127, 0007, Yerevan, Armenia.
Export Citation:
|APA/MLA Format Download EndNote Download BibTex
|MeSH Terms
Carbonic Acid
Cell Adhesion
Drug-Eluting Stents
Middle Aged
Polymers / chemistry*
Titanium / chemistry
Water / chemistry
Reg. No./Substance:
|0/Metals; 0/Polymers; 463-79-6/Carbonic Acid; 7440-32-6/Titanium; 7732-18-5/Water
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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text: Pretoria - Municipalities are owed a staggering R37.7bn by households, while the government owes them about R3.4bn, according to a report released by the National Treasury on Thursday. It showed that total aggregated consumer debt to municipalities and metros stood at R62.3bn as at September 30. Of this, the government accounted for R3.4bn or 5.5%. Households accounted for the largest component, at R37.7bn or 60.6% of the total. The budget statement for local government for the first quarter of the 2010/11 financial year showed metropolitan municipalities were owed a total of R35.4bn at September 30. This is an increase of R3.9bn or 12.4% from the same period last year. The biggest percentage growth from the previous year was in the City of Johannesburg, where it went up 23.5% or R2bn. Nelson Mandela Bay's (Port Elizabeth's) debtors' book increased 16.5% or R275m, the Ekurhuleni metro's 15.1% or R1.1bn and Cape Town's by 11.8% or R558m. The statement covers revenue and expenditure, and conditional grant spending of municipalities for the period July 1 to September 30 2010.


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I cannot print coupons from the Sav A Lot site,as their is no option to do so.There used to be,but for some reason,it never worked.I e-mailed them about this,but got no response.
Okay I am a patient person till I have been sitting on here for hours and that is not a lie! I have yet to figure out the option for coupons and the prices.....why doesn't save a lot show all of there prices. YOU should be proud. We can actually save money in your store and we are proud to do so but Ineed the pricing and the coupons.....please email me at firstname.lastname@example.com and please take the time to explain.....I took the time to do a large list, this is all I ask of you! Thank you so much!
How do you get coupons? Please email me email@example.com thanks
I am very disappointed with Save A Lot, still no coupons to print out and it was saving us some money at the beginning when I signed up. I've emailed them over and over and they didn't help me. There prices have gotten higher and higher each week.
grannytertel FL
sooo where r the coupons?????