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Backpacker Magazine – September 2008
Gas prices are soaring. Glaciers are melting. What's a conscientious hiker to do? Take the bus, says Dan Koeppel, who did just that to escape downtown L.A.
More Mass Transit Hikes
Download more hikes, all accesssible by bus, right here.
More Photos
See more of photographer MIchael Darter's photos from this assignment.
THERE'S NOTHING LIKE A DONUT IN THE WILD. Or an order of onion rings, a Big Mac, or a Grand Slam breakfast. But our time–at a trailhead marked by a quartet of fast-food restaurants, two gas stations, and a giant billboard advertising a radio program hosted by the "boogieman of the morning"–is short. Five backpackers are about to load into what might be the world's most unlikely hiking shuttle: Metro Bus 91, a commuter line that carries a quarter-million passengers annually along a 20-mile route that leads from bustling downtown Los Angeles to the city's suburban foothills.
We are not alone. A dozen strap-hangers wait with us at the intersection. There's a mother with three children; a middle-aged man in a wrinkled suit; and a heavyset teenager with a bike. I count four iPods, six shopping bags, and one Spiderman book tote. We're the most burdened of all, with our fully loaded backpacks. It's a Saturday morning, and we've been traveling for almost two hours, since 6 a.m., when we started our journey on Sunset Boulevard, two blocks from my house and a mile from the Hollywood Freeway.
We step on board, forsaking fast-food delights. The orange vehicle plods along. It's standing room only: We're standing, and we take up all the room. As passengers squeeze around us, we do an awkward dance trying not to whack them in the heads. Soon we'll come to Foothill Boulevard, the main So-Cal thoroughfare to the 650,000-acre San Gabriel Mountains, on the southern fringes of Angeles National Forest. Our stop is coming up. We can see 6,000-foot peaks. And a Starbucks.
ANGELES NATIONAL FOREST IS WHAT LOCAL USED-car dealers like to call "freeway close." That means an easy drive, no matter the distance. But proximity can be problematic. Annually, 30 million people visit the forest, which is located entirely in Los Angeles County. Assuming the average roundtrip to the trailhead is 50 miles, these visitors create roughly 2.25 billion pounds of greenhouse gases. During the 15 years I've lived here, I've been as guilty as the next guy, putting thousands of extra miles on my car as I've repeated the 20-mile back-and-forth from my door to the trailheads.
But it was spiking gas prices that finally made me try to find a better way. I started by selling my car. I live with my girlfriend, so we figured one vehicle would be sufficient. Los Angeles has a new subway, plus those poppy-colored buses, and I own a swell bicycle. I'm also a rabid walker. In 2002, I began climbing the hills in my neighborhood, which are lined with staircases. Five days a week, I hiked them with a GPS, developing a 20-mile, 50-staircase route that gained 7,000 feet. (I wrote about that endeavor for BACKPACKER's June 2004 issue, and have since added 20 more staircases.)
With all this low-impact travel under my belt, I figured the next step was totally logical: Find a way to get to my favorite trailhead in a vehicle that was already going there.
Yep. been there done something like that. Different area.
Take the Mammoth Lakes bus to Lake Mary/Coldwater Campground to trailhead. Hike up over Duck Lake pass, down the othere side, along Cascade Valley/Fish Creek. End up at Red Meadows. Catch the Devils Postpile shuttle bus back to Mammoth Mountain ski lodge parking lot. Then bus back to town.
Getting to Mammoth Lakes, fly from LA, Orange COunty, San Jose, to Mammoth/Yosemite airport. Short cab ride to Mammoth Lakes.
Or there is a bus From Mojave to Mammoth Lakes, too.
WOW! This article was written in 2008. I feel like a jerk.
WOW! This seems like a great idea. As a matter of fact this seems like the exact same idea I emailed to Backpacker several months ago as a story to do. I've been busing it to the mtn's for over 20 years now. I don't know how it is where you all live but for me having a major hub by it gives me the ability to start on one end of the park and finish a couple to a few days later on another end of the park. This hub also reaches a few different parks. The bus doesn't go near every trailhead therefore at times I will get off in a town and get a cab to the trail. On occasion I was fortunate to meet a local willing to give me the ride in exchange for their opportunity to tell some childhood experience about the mtn's or some special spot to explore which I always enjoy. Locals usually refuse to take money so I secretly put it next to them when their not looking. When I started doing this it had nothing to do with being environmentally friendly sorry to say. It was more about never having to backtrack the same trail to the car. Keeping the journey fresh for end to end was always my goal.
Nice Article! Trying to plan a trip for this month.
You all might find this interesting:
University of Southern California
Bay Area to Yosemite. This takes some planning and layovers, but I think is a good option. AMTrack to Yosemite. The Train stattion is in Emeryville across th ebay but AMTrack includes a bus ride over. Take the train to Merced and then a bus to The Valley or t Toulomne Meadows (summer only). I have flown into other cities and rented a car to then visit National Parks. The biggest hassle is yo ucan't carry fuel so you have to plan exacly where you can buy and when. Fuel bottles must be washed with soap and water and air dry to bring on plane. One option is to donate the fuel and bottle to other hikers at the end of the trip.
Two trips I'm Planning using Mass tranist. Pt Reyes Backpacking overnight. Make a reservation first and check bus schedules for Golden Gate Transit. There are only 4 legal overnight campgrounds, all starting from the Visitor center. From downtown San Rafael Transit Hub GGB Transit $2 one way to visitor center. About one hour 20 miles through Samuel P Taylor State Park. You can also spend a night here or in Olema at a private campground. Non weekend days you will likely have the palce to yourself. Summer may be very foggy all day along the coast here. A tent is mandatory (in my opinion) year round due to fog and mist. I've been to Wildcat 6 times and Coast 1. Glen and Sky are short hikes and you can day hike several miles to ocean from here. From SF you can also catch GGB to San Rafael, ferry to larkspur and hike 3 miles to downtown, or Greyhound from SF. Also, if you are coming from SFO, Marin Transporter. From East Bay, Bart to Richmond then GGB to San Rafael. Southbay, Take Caltrains to SF. (As far south as Gilroy and San Jose).
in the philippines, we do it most of the time. it's quite useful especially when traversing a mountain, wherein the jump off town is different from the nearest town where we descend.
I have only taken the bus to a trailhead once, in Vancuver to the Grouse Grind Trail. Having lived in LA from 1977, I have spent much time in the trails of the Algeles. I read your artical with pleasure tracing your rote in my mind. I would have liked a few more waypoints. From Condor Peak, did to head out toward Messenger Flats and the PCT over Mt. Gleason? If so, you must have desended down either 4N32 or 4N24 at the Fire Camp to reach Acton?
I definitely read your staircase article and loved it! This one is great too. Thanks. I live in VT. There's no bus to the trailhead!
Dan - thanks for the good article. You are certainly part of the solution. Hopefully, more than a few people heed your wise words. If so, the planet will be that much greener.
Hey Dan its nice to meet someone who likes to figure out public transportation as much as I do. I can spend hours plotting a trip in LA to the beach or Dodgers stadium using busses and trains; then when I share this info with someone they think I'm crazy. Everyones response is just drive there!


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Siobhan Davies Studios
Siobhan Davies Studios
85 St. George's Road
Greater London
General enquiries
020 7091 9650
Siobhan Davies Dance is one of the country's most outstanding and innovative dance companies and choreographer Siobhan Davies advocates for the wider recognition of dance as a significant and extraordinary art form. The Company's RIBA award-winning building, Siobhan Davies Studios in Southwark, South London, provides a local, national and international resource for learning about movement and dance, and a meeting ground to discuss new ideas. It presents a varied programme of events, performances, talks, artists' sharings and visual art exhibitions.
Venue Type:
Gallery, Artist studio or collective
Mon - Thurs, 9.00 - 22.00
Fri - Sat, 10.00 - 17.00
Sun, 9.00 - 20.00
Additional info
Our kitchen is available for public use.
We also have two public computers with free internet access.
Daniel Lobb | As above, so below
- 5 March — 9 September 2015
Landscape designer and sculptor Daniel Lobb creates a large-scale installation and internal water cycle which extracts the humidity generated from the sweat and breath of dancers in the Studios to sustain plant colonies within a suspended copper rill.
Free entry
Exhibition dates: 15 May – 21 September
Artist in Conversation: 30 May, 7pm
Exhibition Tour: 17 June, 2pm-3pm
This exhibition is part of Human-Nature: art, horticulture & choreography across the growing season, a new year-long series of exhibitions, talks, workshops and performances produced by Siobhan Davies Dance exploring the dynamics of the relationship between people and plants.
Suitable for
- Family friendly
To book for the exhibition tour and the artist talk, please call 020 7091 9650.
To hand: live installation
- 20 September 2014 12-4pm
Dance artist Matthias Sperling performs live durational work To hand as a counterpoint to Body & Void: Echoes of Moore in Contemporary Art, The Henry Moore Foundation's ground-breaking exhibition that makes connections between architect Moore's investigation of internal space and its relationship with the human body.
To hand focuses on creating simple movements and draws attention to a complex collection of decisions in order for Sperling to navigate through the exhibition space.
Suitable for
- Family friendly
The Henry Moore Foundation
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Change correct spelling of stationery to stationary
Twentieth century dictionaries define stationary as not mobile, and stationery as writing paper and envelopes. The word \"stationery\" however was originally spelled with an \"a\" in English. It derived from the fact that such products were sold in \"stationary\" shops and not from travelling peddlers. Both spelling derive from the Latin stationarius defined as a place where something is located. A look at Internet search patterns indicates that more users search for stationary than stationery. This ranges from over twice as many searches for \"email stationary\" than \"email stationery\" to an approximately 6% preference for \"business stationary\" over \"business stationery\".
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NYC Parks Events Calendar
Get up, get out, and do something! Just about any day of the year, you can find something fun, informative, and healthy to enjoy at an area park. Feel free to browse the listings below, or use the search tools to find an event that matches your interests and location.
Viewing 21–30 out of 17,855 events
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Saturday, July 20, 2013
Arty Hours
at The Lawn (in The High Line), Manhattan
10:00 a.m.–12:00 p.m.
Go on a kid-friendly scavenger hunt for High Line Art, then create your own masterpiece inspired by the High Line.
Category: Arts & Crafts, Kids
Bryant Park Moves with Limon Dance
at Bryant Park Lawn (in Bryant Park), Manhattan
10:00 a.m.–11:00 a.m.
Experience the joy of movement and dance with Limon Dance Company.
Category: Dance
at Pier 2 Dock (in Brooklyn Bridge Park), Brooklyn
10:00 a.m.–3:00 p.m.
Get out on the water for kayaking with the Brooklyn Bridge Park Boathouse.
Category: Kayaking and Canoeing, Waterfront
Summer Lawn Greening
at Pier 1 (in Brooklyn Bridge Park), Brooklyn
10:00 a.m.–1:00 p.m.
Pier 1's lawns are a beautiful spot to picnic, lounge, or enjoy amazing views. Help us keep these organically maintained lawns lush and healthy by removing invasive turfgrass…
Category: Nature, Volunteer
2013 Fitness on the Terrace
at Astoria Pool Terrace (in Astoria Park), Queens
10:00 a.m.–11:00 a.m.
Astoria Park Alliance & Central Astoria Local Development Coalition presents Fitness on the Terrace - Yoga
Category: Fitness, Outdoor Fitness
Shape Up NYC: intenSati
at Locomotive Lawn (in Riverside Park South), Manhattan
10:00 a.m.–11:00 a.m.
Combining spoken affirmations with simple choreography, intenSati provides a heart-pumping, exhilarating workout that builds physical, mental, and spiritual muscle.
Category: Fitness, Outdoor Fitness
City of Water Day
at Sebago Canoe Club Clubhouse, Brooklyn
10:00 a.m.–4:00 p.m.
City of Water Day open paddle with the Sebago Canoe Club, National Park Service, and Regional Plan Association. Come experience activities like sailing, canoeing, kayaking and rowing.
Category: Education, Nature, Fitness, Tours, Kayaking and Canoeing, Waterfront
Shape Up NYC: intenSati
at Locomotive Lawn (in Riverside Park South), Manhattan
10:00 a.m.–11:00 a.m.
Combining spoken affirmations with simple choreography, intenSati provides a heart-pumping, exhilarating workout that builds physical, mental, and spiritual muscle.
Category: Fitness, Outdoor Fitness
Aerobics Class
at Poe Park Visitor Center (in Poe Park), Bronx
10:00 a.m.–11:00 a.m.
Come have fun, get fit and healthy with our aerobics instructors
Category: Fitness, Outdoor Fitness
Wave Hill Family Art Project: Water, Water Everywhere
at Wave Hill House (in Wave Hill), Bronx
10:00 a.m.–1:00 p.m.
Sketch the river landscape and Wave Hill's Aquatic Garden, and discover that water really is everywhere.
Category: Arts & Crafts, Nature, Kids
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Crest Vent
The Crest Vent is nautical miles ahead of anything else in your closet when it comes to style and performance. Featuring a waterproof leather or synthetic upper, the Crest Vent's classic look is supported by modern Sebago® Blue Wave comfort technology, an Energy Return heel pad, and slip-resistant, non-marking Sebago® TriWater™ Sole.
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Luis E.
LOVE these shoes! I get tons of complements and they're ever so comfortable! I was also wondering how to clean them since my last pair of boat shoes lost their colors after washing them. A good question would be: Are these shoes washable or what would be proper care instructions? Frankly, that's the only thing that I wish came with my order (done about 2 months ago). I had a bunch of return labels, but I really needed care instructions. Perhaps something you guys can include for my next orders. Cheers
We are happy to hear you enjoy the shoes so much! We appreciate the feedback about including the care instructions. We will be in touch with you soon to offer help.
Product Size Rating:Sized as Expected
How do you most use this product?:Work, going out.
Cleaning crest vent
Hi sebago First of all I'd like to say that I love these crest vents. They look really good and at the same time they are very comfortable to wear. I bought mine almost 3 months ago and have worn it every chance I get. However I just want to ask how do you clean these shoes? Can i just use soap and water and toothbrush to remove the dirt from the 'suede' top and the sides of the shoes? Would like to know your answer on this. Thanks
We are thrilled to hear you have enjoyed this style so far and that they are super comfortable. To clean the footwear you can use warm water and a diluted soap to gently wash the outside. For more detail give our Customer Service Team a call at 1-866-699-7367.
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Great looking, but feet got hot
I bought these shoes in Navy. The size was perfect and the shoes look amazing. However, I bought it hoping that the "vent" would keep my feet cool. This wasn't the case. My feet felt way hotter in these shoes than any of my other non-vent shoes. It was cold in my office and the rest of me was shivering, but my feet were sweating in the shoes. I'm not sure whether to return the shoes or punch holes in them :(
Our lightweight Triton Three-Eye or Carrick Three-Eye may work better for you. Give our customer service team a call with questions at 866-699-7367.
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Widmer Hefeweizen - Widmer Brothers Brewing Company
Displayed for educational use only; do not reuse.
Ratings: 1,728 | Reviews: 758 | Display Reviews Only:
Reviews by jesseejames:
4.43/5 rDev +34.7%
Widmer Hefeweizen is one of my favorite american beers. It has a wonderful smell and nice creamy rich color. It is very drinbkable and is not overhopped like most smaller brewing company's are. I thought that this beer had a wonderful head that can only be appreciated if you pour it into a glass first. I think that most beers are improved by releasing them from the bottle before drinking.
05-27-2013 18:40:40 | More by jesseejames
More User Reviews:
2.5/5 rDev -24%
Appearance Light copper in color and cloudy with a decent head that went down rather quickly.
Smell The aroma is very faint. Theres a touch of yeast in there but the dominant scent is orange/citrus. Theres also some light spicing.
Taste Wheres the wheat? The orange flavors come out more followed by a hop backbone. Ist das ein hefeweizen?
Mouthfeel Wheres the carbonation? This bottle is flat as a pancake. Its very thin in the mouth and uninspiring.
Drinkability I cant imagine ever wanting to buy another one of these. This was lousy.
Sinkability I rate this a 4.5 here. It has a very good chance of cleaning my kitchen pipes tonight.
10-11-2003 00:55:16 | More by RoyalT
1.63/5 rDev -50.5%
Pale yellow-orange body with a big white head that quickly dissipates to nothing. Extremely cloudy. Rather rotten and heavily yeasty aroma of oranges, lemon, and cat hair. Very offensive and engineered. The yeast seems infected. There is no banana. Flavor is rotten fruit and wheat (not in a good way) with only minimal pepper and clove. Greater bitterness than most hefes but overall rather bland and too sweet. Thick mouthfeel. Very disappointing on multiple occasions. Nearly wretched.
08-16-2006 14:03:30 | More by DaPeculierDane
3.03/5 rDev -7.9%
Virtually no head, but plenty of carbonation present on sight. No real lacing to speak of. A pale and hazy straw color that looks weak and watery.
A weak banana and spicy clove aroma in addition to pretty strong grain and wheat smells. Nothing overpowering in terms of aroma.
The flavors begin with a bit of lemon that quickly gives way to a mild banana. That quickly gives way to a sharp clove spiciness. The strength of the clove surprised me compared to the ale's other watered down components. There's also a lot of wheat flavors, some of which aren't too flattering. The right flavor aspects are present, just out of balance.
Grainy mouthfeel, but still light on the palate with just the right amount of carbonation.
It's a light and refreshing beer for the summer, but I couldn't see myself having more than one of these a sitting, nor would I really go back to it in the future. This is not a beer to seek out in terms of representing the style.
04-10-2012 02:07:17 | More by ExtraStout
3/5 rDev -8.8%
01-19-2013 02:41:14 | More by tbryan5
3/5 rDev -8.8%
06-20-2014 05:34:30 | More by BubalooBrewMaster
3.9/5 rDev +18.5%
Presentation: 12 oz short brown twist with an ink jet printed drink before date above the label.
Appearance: Cloudy orange gold with a clinging bubbly white lace.
Smell: Fruity with mild citrus, hints of malted wheat and a touch of yeast.
Taste: Very smooth (almost creamy) and medium bodied, mildly crisp up front with a light bite of grain and yeast. Then comes some fruit, malted wheat, bread/biscuit and a flavourful hop bitterness (citrusy). Faint rustic under-tones appear from the flavour of the yeast and linger with some grain and a soft spicy flavour.
Notes: A simply amazing brew ... brewed with an Altbier yeast strain and hopped with Tettnanger and Cascade hops to make for an unequaled brew amongst the many American wheat beers. This was proven at The 1998 Great American Beer Fest by being awarded a gold in the American wheat category. Top pick for American wheat beers!
07-17-1999 00:00:01 | More by BeerAdvocate
3.8/5 rDev +15.5%
A very good hefe. This beer poured a great murky medium gold color with a decent pillowy white head that left a good ammount of lace on my glass. The smell was quite citrusy with some hop scent as well. The taste was quite good with a great citrus bite, spicy flavors and a good bit of hoppieness. A good beer that usually sells for a reasonable price as well.
05-04-2004 10:04:15 | More by Dmann
3.5/5 rDev +6.4%
06-13-2012 00:43:51 | More by Carissa
3.5/5 rDev +6.4%
01-31-2013 01:36:02 | More by Lazaro
2.63/5 rDev -20.1%
Out with Redhook's wheat and in with Widmer's Hefeweizen! Thanks to Anheuser-Busch ... and at least on the East Coast.
12oz brown bottle. Freshness embossed on the front of the label.
Extremely cloudy and straw light amber, topped with a creamy white lace; color and suspension of particles seemed contrived ... it poured cloudy, after settling in the fridge for days; odd, didn't need any rousing. Light citrus, wheat and faint clove in the aroma; weak overall. Clean, crisp carbonation and somewhat smooth with a pear-feel on the palate later. Sharp citric flavour upfront, that fades very quickly and allows a rather bland malt profile of wheat tannins and dry grain to come through and dominate. Light and short lived spice. Touch of fruitiness, but none of the expected banana or clove of a true "Hefeweizen." Okay, there's some light banana, but it's very weak, and the spice is more generic than distinct like clove. Notes of gum can also be detected as the beer warms, as well as some depth of pale malt sweetness. Finish is dry, with linger wheat and spice; not pleasant; mouthful of wheat husk; odd.
Tired of American breweries brewing a wheat beer and calling it a Hefeweizen? Then you can probably skip this beer. Otherwise, give it a try. It's average at best, with only hints of traditional style, but that's okay ... It's still enjoyable and I recommend that you let the beer warm a bit to loosen up on all of those tannins and allow some of the sweetness and other nuances to emerge.
08-06-2003 20:25:46 | More by Todd
4/5 rDev +21.6%
Have to agree with the bros on this, that this beer is slightly better a tad warmer than most like. right off the tap, in an iced glass, this beer looses a lot of it's characheter. it's still very drinkable, but you wont get the true taste that it is should to have. Other than that it is basicly the same as in the bottle. all around decent version of the classic heffeweizen. never had sam adams heffeweizen on tap, but im sure it would be better.
06-30-2005 03:33:45 | More by twi1609372
2.33/5 rDev -29.2%
This is a tough one. It's hard to know if I should review this as a Hefeweizen or as an "American Wheat Beer." If I were to review it as the former - it would be unsatisfactory. As the latter - it's perhaps the epitomy of the style. Given that I think that the emerging style of the "American Wheat Beer" is marginal at best, I guess I'll review it as a Hefeweizen and thus do double service as both a review and a comment on the style.
Initial pour shows an odd and almost bright orange colour with the only similarity to a Hefeweizen being its cloudiness. Little to no head that quickly fades to a thin but slightly clingy lace. Aromas are predominantly yeast and fruit with an undercurrent of malt and the slightest hint of wheat/grain.
First tastes are of a mild crispness and yeast, smooth and mid-bodied. This promises a flavorful beer, but this hope is dispelled by the following blast of hops, which overwhelm the fruit, wheat and malt that should define the style. The finish is dominated by the fading bitterness from the hops and an odd "off" flavour that could well be from the yeast.
Sigh... not to my taste.
03-26-2003 22:35:13 | More by SamuraiJack
4.5/5 rDev +36.8%
04-28-2013 05:05:00 | More by TTripp725
New York
4.05/5 rDev +23.1%
Presentation: It was poured from a brown 12oz bottle into a weizen glass. The label has a bottled on date but no abv%.
Appearance: The body has a cloudy orange/yellow body with fine yeast sediment hanging in suspension. On top sits a modest one inch tall collar of creamy white foam. This head quickly settles down to thin film layer that make some slick glass lacing.
Smell: I get a light lemon like citrus and wheat bready character with some mild clove and a very slight bubble gum and banana.
Taste/Palate: It starts with a light and sweet wheat base. From there it adds some citrusy orange and lemon character as well as some very slight bubble gum and banana. (The classic Hefeweizen bubble gum/banana notes are much thinner than I would like to see.) It then finishes with some dry spice and a nice balance of leafy hop bitterness. The palate is fairly crisp and very quaffable.
Notes: As a Hefeweizen it is average but as an American Wheat Ale it is very well made.
04-13-2011 16:44:24 | More by generallee
4.5/5 rDev +36.8%
06-30-2013 23:00:22 | More by ValpoExpo
3.5/5 rDev +6.4%
08-27-2013 03:27:11 | More by nstroup
3.5/5 rDev +6.4%
10-25-2013 03:58:39 | More by TimoP
2.25/5 rDev -31.6%
07-17-2014 02:23:11 | More by friggz81
3/5 rDev -8.8%
11-15-2012 22:36:41 | More by VernonKell
3.25/5 rDev -1.2%
02-07-2013 22:01:51 | More by Jumjum
3.98/5 rDev +21%
12oz brown bottle with a freshness date, served sans lemon.
LOOK: Opaque pale amber, excellent head.
SMELL: Bready wheat, faint bubble gum, vague ripe fruit, neutral yeast and some pizza dough
TASTE: Heavenly smoothness, moderate body, bready, grainy, assertive hop bitterness, slightly herbal, ripe fruit, spice, bubble gum, light tartness, yeast, drying finish
A highly underrated beer style or perhaps an overly disliked or misunderstood style. For what it is, Widmer brews a great one.
10-18-2012 00:18:09 | More by Jason
3.1/5 rDev -5.8%
Had never seen this before in Kentucky, but it was all over Lexington, this weekend, even sold in quik marts. One of the Macro companies must have got their hands on distribution. 12 oz bottle pours a hazed, straw yellow body with a quickly falling, offwhite head. Some spots of patch lace get left on the glass.
Aroma is very subdued, with hints of lemon and orange.
Mouthfeel has good carbonation and is light bodied.
Taste is citrusy lemon with a wheat background. The hops impart some white pepper. Crisp and refreshing, and goes down smooth. No offnotes, but not very complex.
06-05-2004 22:29:51 | More by merlin48
New York
3.83/5 rDev +16.4%
12 ouncer, with bottled on dating prominently on the bottom of the front label. Pours cloudy darker apricot. Minor off white head, and just a few smudges of lacing, The nose is full of citrus, cloves and coriander. Pretty for the style. Pleasant enough Hefe, more lemon, clove and spice on the palate. Thirst quenching summer quaffer. Finishes with a respectable and quite drying hop crackle. Nice American Wheat. Suprised by the super low ratings for this at least respectable ale
06-13-2009 08:07:53 | More by Billolick
3/5 rDev -8.8%
02-16-2014 22:51:49 | More by KolbMarley
Widmer Hefeweizen from Widmer Brothers Brewing Company
75 out of 100 based on 1,728 ratings.


text:
MCB to dance Tharp-Byrne workMonday, January 11th, 2010
Miami City Ballet's Edward Villella is particular about the choreographers he adds to the company's George Balanchine-rooted repertoire. Twyla Tharp is one of the favored few.
Program II, performed Jan. 15-17 at the Kravis Center, will feature the company's first performances of Tharp's The Golden Section (at right in a photo by Joe Gato). The dance-theater piece is excerpted from Tharp's acclaimed full-evening The Catherine Wheel, a collaboration with David Byrne of the Talking Heads.
According to Tharp, the dancers perform in "an abstract arena of pure energy." Bathed in golden light and looking like Olympiads, they storm the stage to execute daring, closely coordinated feats.
Another dramatic piece on the program is Balanchine's Slaughter on Tenth Avenue. This, too, was part of a larger work – in this case the 1936 musical comedy On Your Toes, Balanchine's first Broadway venture. Performed to music by Richard Rodgers, the work takes place in a night club and features gangsters, cops, a stripper and a tap dancer.
The other works on the bill are also by Balanchine and are more typically balletic. They are Divertimento No. 15, set to Mozart's work by the same name, which Balanchine called "probably the finest (divertimento) ever written," and Valse Fantaisie, set to Mikhail Glinka's Valse Fantaisie in B minor.
For information, call Miami City Ballet's box office at (877) 929-7010, visit www.miamicityballet.org, or call the Kravis at 832-7469.


text:
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AleSmith Decadence 2006 (Dead By Dawn) Barrel Aged - AleSmith Brewing Company
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Ratings: 16 | Reviews: 9 | Display Reviews Only:
Reviews by pmarlowe:
District of Columbia
4.03/5 rDev -3.8%
On tap at AleSmith during 2011 San Diego Beer Week. Advertised as having a "pleasing tartness". Uh oh, red flag.
Pours opaque amber with a solid cap of sand colored foam. Good retention and minimal lacing. Smells like rich caramel, sweet cherry, sugar coated plum/raisin, and some oak and dark chocolate. Delicious, although not a ton of barrel character. Taste is tart cherry and some caramel malt. The cherry is quite tart, carries through most of the sip, and lingers for awhile. It's not unpleasant, but kind of masks any other complexity that might be there, including I'm guessing the barrel. Medium body and medium-light carbonation which is pretty smooth. Overall, this is pretty good: you can tell there's a great beer underneath somewhere, but the tartness kind of makes it one dimensional.
11-07-2011 01:03:05 | More by pmarlowe
More User Reviews:
5/5 rDev +19.3%
11-26-2011 22:11:10 | More by GarrettB714
3.28/5 rDev -21.7%
On tap at Alesmith
Look: Dark brown in color with a 1/4 inch tan head and great retention with some spotty lace
Smell: Pleasant sourness and a bit of vinegar which hides most of the other scents but there is some caramel mixed in
Taste: The beer starts our a bit a funky sourness that is not over powering like most sours. The middles carries a slight acidic vinegar note. And the beer finishes with a nice caramel toffee backbone
Mouthfeel: Medium body and carbonation. A bit tart and funky
Overall: Very interesting beer that was actually better than I thought it was going to be
11-15-2011 01:25:44 | More by DarthKostrizer
4.33/5 rDev +3.3%
Wow... '06 decadence?! What a treat. Walked into the brewery and saw this gem up on the tasting board. They poured about a 3oz taste for me.
Looked very full of body with a rich brownish-pink color and pinkish-tan head.
Smelled interesting. Dark fruits and wood. A little booziness from the bourbon perhaps?
Taste took my mouth on a roller coaster. Almost reminds me of my V009 experience. Think Charlie and the Chocolate Factory and the Thanksgiving meal gum. Flavors keep changing and playing off of each other. Figs, cherries, raisins and grapes. Just a hint of bourbon in the background with some of the woody barrel flavors and vanilla creeping in.
The flavors are sticky to the mouth and replay even after your sip is down the hatch. Nice carbonation on this one as well.
Super glad I was able to try this one at Alesmith. Wish it was a regular tap resident. Hope they uncover another keg of this soon.
09-18-2011 06:45:07 | More by cocoapuph
4.25/5 rDev +1.4%
Sampled at AleSmith during San Diego trip.
A- Dark red body out of the tap with a big dark tan head. Silky head with creamy texture and good size and retention. Good fine lace rings.
S- Sour fruit and subdued bourbon oak barrel. Very aromatic with a nice backbone of old caramel malts, like an old ale would have.
T- Sour fruit, white grapes and apple notes come with a nice tartness probably from an infection. Subdued bourbon, oak and vanilla from the barrel. The base beer seems to be old caramel and raisin forward.
MF- Silky, oily light body with a great tartness. Some bitterness in the finish.
Interesting sour and bourbon blend. Also takes on a slight old ale caramel aspect.
10-30-2011 23:57:27 | More by cbutova
5/5 rDev +19.3%
02-18-2012 00:39:19 | More by nasa258e
4/5 rDev -4.5%
12-27-2011 22:18:33 | More by wattershed
4.35/5 rDev +3.8%
Dark copper/brown pour with a very creamy looking off white head.
Obviously the hops are gone. Sweet malts and some sourness come through.
A lot of sweet and sour. A small amount of bourbon flavor. It's a tough flavor to describe. Very fruity, sour and tasty.
M-Medium smooth body with plenty of carbonation.
O-Not what they intended but it was a good beer to try. Tasty with no bad flavors.
09-02-2011 23:33:09 | More by ZX6Chris
4.5/5 rDev +7.4%
On tap at Alesmith
A: Pretty clear dark brown color with a huge fluffy light brown head.
S: Some great bourbon notes, toasted coconut, vanilla, raisin and some plum.
T: Wow. Amazing complexity. Starts with some roasted malt and a bit of vanilla and then becomes sour as a lot of sour cherry flavors come into play. Bourbon isn't really evident in the taste, but it really made the smell fantastic. Really glad to have gotten to try this one.
10-27-2011 23:17:18 | More by notchucknorris
4.47/5 rDev +6.7%
On tap at the Alesmith Tasting Room
Pours an amber color with a very thick off-white head that leaves a ton of lacing.
Smell is on the lighter side. There is plenty of bourbon, molasses, and some fruit.
Very complex! Dark fruit, vanilla, bourbon, and sour all come together. The dark fruit stands out as being the strongest.
This is very well carbonated. It is rich, creamy, and on the heavier side.
This was one of the most complex beers I've had. Highly enjoyable. A real treat to be able to try.
10-11-2011 23:21:15 | More by fatmcb1
4/5 rDev -4.5%
11-14-2011 17:31:53 | More by khumbard
3.68/5 rDev -12.2%
On tap at Alesmith. Thanks to Chris for the tip. What the hell is this? Decadence Dead By Dawn from 2006 aged in bourbon barrels for over a year. What a pleasant surprise.
A: Dark reddish brown with a big creamy foam head.
S: Chocolate, caramel, vinegar, and bourbon, with big lactic notes. Dark red fruits are powerful, redolent of grape, plum, and currant. Toffee is evident.
T: High level of lactic sourness immediately with bourbon, grapes, and plums. This is very oaky and tannic. Caramel and toffee blend with chocolate and vanilla. The finish is bitter with a somewhat acerbic sourness and a strong acetic note. Alcohol is present in the terminus.
M: Upper medium in body with lower high carbonation.
Overall: The beer doesn't have a high level of drinkability, but it was nice to have six ounces. The sourness is kind of one note and a little harsh with the tannins at times, but there was a lot going on. Definitely worth trying.
09-03-2011 01:53:24 | More by HopHead84
4/5 rDev -4.5%
07-19-2014 06:13:47 | More by zestar
4.13/5 rDev -1.4%
Stopped by Alesmith for some Evil Dead Red and saw this on the board, yes please.
It pours a copper/amber color with a huge frothy off white head that lasts and leaves a very sticky lace. The nose is big and complex with a tart sourness and notes of dark fruits, caramel, molasses, vinegar, bourbon, vanilla, and alcohol. The nose doesn't leave any flavors hidden and puts it all out there for what you will taste, the sourness is great with the dark fruits and vanilla bourbon, the alcohol is there but very well integrated. Its a medium body with a slight chewiness and sticky, well carbonated. I was very happy to get to try this and I wasn't let down it's a very good beer.
09-27-2011 13:38:23 | More by BdubleEdubleRUN
4/5 rDev -4.5%
08-12-2012 12:26:05 | More by t0rin0
4/5 rDev -4.5%
12-23-2011 22:55:56 | More by SanDiegoBeerLove
AleSmith Decadence 2006 (Dead By Dawn) Barrel Aged from AleSmith Brewing Company
90 out of 100 based on 16 ratings.


text:
Town Square
NFL ref strikes more union loons
Original post made by Mack on Sep 29, 2012
Comments (6)
on Sep 29, 2012 at 11:38 am
Okay Mack ... from NFL ref's to someone stealing everyone's money ... to Bart ... back to Obama being the source of all evil.
Any you guys wonder why you're losing AND have lost every major election in recent memory.
Hint: Find some friends with some brains / tell them to talk to you about sensible things like LOGIC / rinse twice and wait until the brain-freeze thaws.
ps: looney tune rights have done so much damage to the Republican state of mind that it may take decades to recover. Good job loons
on Sep 29, 2012 at 3:25 pm
"Any you guys wonder why you're losing AND have lost every major election in recent memory."
How can anyone take your comments seriously when you can't even remember the 2010 elections and the fact that dems were trounced by tea party supported candidates? How soon they forget........must be the 'medicinal pot'........
on Sep 29, 2012 at 4:38 pm
It was a lockout by the owners....not a strike. The owners are to blame for not having qualified refs. Please get your facts straight.
on Sep 29, 2012 at 7:28 pm
Thank you for your clarification. I knew this was a different issue, now I know why.
on Sep 29, 2012 at 9:31 pm
I thought the replacement refs were doing a very fine job. If the owners/NFL had held out a little longer, I think the winds of victory would have pushed them into the winners' circle. Sometimes when it looks like you're behind, you're really ahead.
Vote Mitt -- Guaranteed, he's already got Pennsylvania sewed up! He guarantees it's a lock!
on Sep 30, 2012 at 7:20 am
Marie and Ned,
You'd make good socialists. Call it whatever you want. The UNIONS are to blame.
If you were a member and logged in you could track comments from this story.
Jim Kohnen Post Office Signed into Law
By Roz Rogoff | 5 comments | 1,072 views
Never Say Never -- the Perry Indictment
By Tom Cushing | 7 comments | 788 views
CPRA: Balancing privacy, public's right to know
By Gina Channell-Allen | 3 comments | 657 views
Patience and very deep pockets can pay off
By Tim Hunt | 0 comments | 553 views


text:
The term weapon is generously applied to describe offensive skill plays and occasionally used on defense as well.
Dolphins punter Brandon Fields is an asset of a different kind, but the term still applies.
Hes a huge weapon, kicker Caleb Sturgis said of Fields. When you can turn the field like that, youre going to put yourself in good position.
Its certainly never a good sign for a team to see its punter on the field, but when the situation arises, theres arguably no one better in the league than Fields.
The Michigan State product entered the weekend as the NFLs leader in gross punting average, a simple measure of how far beyond the line of scrimmage the ball travels. Fields is the only punter whose average is more than 50 yards.
At 6-5 and 249 pounds, Fields is one of the biggest punters in league.
That size, combined with the proper form and attention to detail, can send the ball soaring.
Obviously my size helps me being tall, obviously, heavier than some of the other guys, and a lot of it is technique, Fields said. If all that mattered was how big you are, a lot of the linemen would be crushing the ball.
Sturgis, whose rookie leg is nothing to sneeze at, said he was in awe the first time he saw Fields punt in person.
The noise it makes is almost unreal, Sturgis said. It just explodes.
But a bigger source of pride for Fields is net punting, which subtracts yardage for returns and touchbacks. Fields net average of 44.0 yards also leads the league.
I want to try to lead the league in net punting, Fields said. Thats the ultimate of where the ball ends up. But thats a combination of myself and my cover guys.
The seven-year veteran has spent his entire career in Miami, and his gross and net averages have improved year-to-year almost without fail. But despite career bests in both key areas, Fields isnt ready to say that this is his best season.
I would say Ive been doing well, but I havent been perfect out there.
Fields credits his insatiable drive to improve as the reason he has become one of the best in the business. And although specialists are often thought of as separated from the rest of the team they often spend huge chunks of practices on their own Fields equated his work and improvement to that of any other play on the team.
None of the guys here are here because they sit on their butts and do nothing, Fields said. Everybody is working on their craft, one way or another.
Children dont exactly covet posters of punters or dream of delivering six-seconds of glorious hang time in the Super Bowl, so, predictably, Fields realization that punting was his primary craft came gradually.
Although he punted in high school, Fields also played linebacker and was a pretty good pass-blocking offensive tackle. He was quick to remind reporters that a lot has changed since then, almost sensing an upcoming wave of jokes about being the solution to protecting Ryan Tannehill.
Fields abandoned blocking responsibilities and specialized while at Michigan State, and its certainly been a wise career move. Fields is signed through the 2016 season on a contract thats worth north of $14 million.
So whats left to work toward?
As far as personal goals, Fields said he wants to get to his first Pro Bowl. He came up short of that distinction last year, despite leading the league in gross punting average and winning the positions online fan vote, which accounts for one-third of the total selection process.
His three-yard improvement in net average from last year, however, could finally send him packing for Honolulu at seasons end.
In the meantime, he is content to flip field position for a winning team and pin opponents deep in their own territory, which he said is the most satisfying feeling a punter can feel.
When the defensive guys run onto the field, theyre hyped up, Fields said. That obviously feels good, knowing that Im contributing to the team.
Miami Herald sportswriter Adam H. Beasley contributed to this report.


text:
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text:
So pumped to write about a quarterback award that didn't go to Cam Newton. Wisconsin Badgers QB Scott Tolzien won the 2010 Johnny Unitas Golden Arm Award, which is awarded exclusively to senior quarterbacks. Thus frequent nominees Newton, Boise St. Broncos QB Kellen Moore, and Stanford Cardinal QB Andrew Luck were not eligible.
Tolzien led the Badgers to their first Rose Bowl bid in over a decade and a share of the Big Ten title, leading the nation in completion percentage. He threw for only 2,300 yards, but that's about all the Badgers needed from him due to their mighty running game.
Recent Unitas winners have included Texas Longhorns QB Colt McCoy, Texas Tech Red Raiders QB Graham Harrell, Boston College Eagles QB Matt Ryan, and Notre Dame Fighting Irish QB Brady Quinn.
To celebrate the most mature of all college football player awards, party responsibly with Bucky's Fifth Quarter.


text:
This document describes "regular" (variants-only) VCF files. For information on the gVCF format produced by HaplotypeCaller in
-ERC GVCF mode, please see this companion document.
VCF stands for Variant Call Format. It is a standardized text file format for representing SNP, indel, and structural variation calls. See this page for detailed specifications.
VCF is the primary (and only well-supported) format used by the GATK for variant calls. We prefer it above all others because while it can be a bit verbose, the VCF format is very explicit about the exact type and sequence of variation as well as the genotypes of multiple samples for this variation.
That being said, this highly detailed information can be challenging to understand. The information provided by the GATK tools that infer variation from NGS data, such as the UnifiedGenotyper and the HaplotypeCaller, is especially complex. This document describes some specific features and annotations used in the VCF files output by the GATK tools.
The following text is a valid VCF file describing the first few SNPs found by the UG in a deep whole genome data set from our favorite test sample, NA12878:
##FILTER=<ID=LowQual,Description="QUAL < 50.0">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="log10-scaled probability of variant being true under the trained gaussian mixture model">
##UnifiedGenotyperV2="analysis_type=UnifiedGenotyperV2 input_file=[TEXT CLIPPED FOR CLARITY]"
chr1 873762 . T G 5231.78 PASS AC=1;AF=0.50;AN=2;DP=315;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=91.05;MQ0=15;QD=16.61;SB=-1533.02;VQSLOD=-1.5473 GT:AD:DP:GQ:PL 0/1:173,141:282:99:255,0,255
chr1 877664 rs3828047 A G 3931.66 PASS AC=2;AF=1.00;AN=2;DB;DP=105;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=92.52;MQ0=4;QD=37.44;SB=-1152.13;VQSLOD= 0.1185 GT:AD:DP:GQ:PL 1/1:0,105:94:99:255,255,0
chr1 899282 rs28548431 C T 71.77 PASS AC=1;AF=0.50;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=17.94;SB=-46.55;VQSLOD=-1.9148 GT:AD:DP:GQ:PL 0/1:1,3:4:25.92:103,0,26
chr1 974165 rs9442391 T C 29.84 LowQual AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=95.26;MQ0=0;QD=1.66;SB=-0.98 GT:AD:DP:GQ:PL 0/1:14,4:14:60.91:61,0,255
It seems a bit complex, but the structure of the file is actually quite simple:
chr1 873762 . T G 5231.78 PASS [ANNOTATIONS] GT:AD:DP:GQ:PL 0/1:173,141:282:99:255,0,255
chr1 877664 rs3828047 A G 3931.66 PASS [ANNOTATIONS] GT:AD:DP:GQ:PL 1/1:0,105:94:99:255,255,0
chr1 899282 rs28548431 C T 71.77 PASS [ANNOTATIONS] GT:AD:DP:GQ:PL 0/1:1,3:4:25.92:103,0,26
chr1 974165 rs9442391 T C 29.84 LowQual [ANNOTATIONS] GT:AD:DP:GQ:PL 0/1:14,4:14:60.91:61,0,255
After the header lines and the field names, each line represents a single variant, with various properties of that variant represented in the columns. Note that here everything is a SNP, but some could be indels or CNVs.
The first 6 columns of the VCF, which represent the observed variation, are easy to understand because they have a single, well-defined meaning.
CHROM and POS : The CHROM and POS gives the contig on which the variant occurs. For indels this is actually the base preceding the event, due to how indels are represented in a VCF.
ID: The dbSNP
rs identifier of the SNP, based on the contig and position of the call and whether a record exists at this site in dbSNP.
REF and ALT: The reference base and alternative base that vary in the samples, or in the population in general. Note that REF and ALT are always given on the forward strand. For indels the REF and ALT bases always include at least one base each (the base before the event).
QUAL: The Phred scaled probability that a REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is -10 * log(1-p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in 10^10 chance. These values can grow very large when a large amount of NGS data is used for variant calling.
FILTER: In a perfect world, the QUAL field would be based on a complete model for all error modes present in the data used to call. Unfortunately, we are still far from this ideal, and we have to use orthogonal approaches to determine which called sites, independent of QUAL, are machine errors and which are real SNPs. Whatever approach is used to filter the SNPs, the VCFs produced by the GATK carry both the PASSing filter records (the ones that are good have PASS in their FILTER field) as well as those that fail (the filter field is anything but PASS or a dot). If the FILTER field is a ".", then no filtering has been applied to the records, meaning that all of the records will be used for analysis but without explicitly saying that any PASS. You should avoid such a situation by always filtering raw variant calls before analysis.
For more details about these fields, please see this page.
In the excerpt shown above, here is how we interpret the line corresponding to each variant:
The genotype fields of the VCF look more complicated but they're actually not that hard to interpret once you understand that they're just sets of tags and values. Let's take a look at three of the records shown earlier, simplified to just show the key genotype annotations:
chr1 873762 . T G [CLIPPED] GT:AD:DP:GQ:PL 0/1:173,141:282:99:255,0,255
chr1 877664 rs3828047 A G [CLIPPED] GT:AD:DP:GQ:PL 1/1:0,105:94:99:255,255,0
chr1 899282 rs28548431 C T [CLIPPED] GT:AD:DP:GQ:PL 0/1:1,3:4:25.92:103,0,26
Looking at that last column, here is what the tags mean:
GT : The genotype of this sample. For a diploid organism, the GT field indicates the two alleles carried by the sample, encoded by a 0 for the REF allele, 1 for the first ALT allele, 2 for the second ALT allele, etc. When there's a single ALT allele (by far the more common case), GT will be either:
GQ: The Genotype Quality, or Phred-scaled confidence that the true genotype is the one provided in GT. In the diploid case, if GT is 0/1, then GQ is really L(0/1) / (L(0/0) + L(0/1) + L(1/1)), where L is the likelihood that the sample is 0/0, 0/1/, or 1/1 under the model built for the NGS dataset. The GQ is simply the second most likely PL - the most likely PL. Because the most likely PL is always 0, GQ = second highest PL - 0. If the second most likely PL is greater than 99, we still assign a GQ of 99, so the highest value of GQ is 99.
AD and DP: These are complementary fields that represent two important ways of thinking about the depth of the data for this sample at this site. See the Technical Documentation for details on AD (DepthPerAlleleBySample) and DP (Coverage).
PL: This field provides the likelihoods of the given genotypes (here, 0/0, 0/1, and 1/1). These are normalized, Phred-scaled likelihoods for each of the 0/0, 0/1, and 1/1, without priors. To be concrete, for the heterozygous case, this is L(data given that the true genotype is 0/1). The most likely genotype (given in the GT field) is scaled so that it's P = 1.0 (0 when Phred-scaled), and the other likelihoods reflect their Phred-scaled likelihoods relative to this most likely genotype.
With that out of the way, let's interpret the genotypes for NA12878 at chr1:899282.
chr1 899282 rs28548431 C T [CLIPPED] GT:AD:DP:GQ:PL 0/1:1,3:4:25.92:103,0,26
At this site, the called genotype is
GT = 0/1, which is C/T. The confidence indicated by
GQ = 25.92 isn't so good, largely because there were only a total of 4 reads at this site (
DP =4), 1 of which was REF (=had the reference base) and 3 of which were ALT (=had the alternate base) (indicated by
AD=1,3). The lack of certainty is evident in the PL field, where
PL(0/1) = 0 (the normalized value that corresponds to a likelihood of 1.0). There's a chance that the subject is "hom-var" (=homozygous with the variant allele) since
PL(1/1) = 26, which corresponds to 10^(-2.6), or 0.0025, but either way, it's clear that the subject is definitely not "hom-ref" (=homozygous with the reference allele) since
PL(0/0) = 103, which corresponds to 10^(-10.3), a very small number.
Finally, variants in a VCF can be annotated with a variety of additional tags, either by the built-in tools or with others that you add yourself. The way they're formatted is similar to what we saw in the Genotype fields, except instead of being in two separate fields (tags and values, respectively) the annotation tags and values are grouped together, so tag-value pairs are written one after another.
chr1 873762 [CLIPPED] AC=1;AF=0.50;AN=2;DP=315;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=91.05;MQ0=15;QD=16.61;SB=-1533.02;VQSLOD=-1.5473
chr1 877664 [CLIPPED] AC=2;AF=1.00;AN=2;DB;DP=105;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=92.52;MQ0=4;QD=37.44;SB=-1152.13;VQSLOD= 0.1185
chr1 899282 [CLIPPED] AC=1;AF=0.50;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=17.94;SB=-46.55;VQSLOD=-1.9148
Here are some commonly used built-in annotations and what they mean:
|Annotation tag in VCF
|See the Technical Documentation for Chromosome Counts.
|If present, then the variant is in dbSNP.
|See the Technical Documentation for Coverage.
|Were any of the samples downsampled because of too much coverage?
|See the Technical Documentation for SpanningDeletions.
|MQ and MQ0
|See the Technical Documentation for RMS Mapping Quality and Mapping Quality Zero.
|See the Technical Documentation for Base Quality Rank Sum Test.
|See the Technical Documentation for Mapping Quality Rank Sum Test.
|See the Technical Documentation for Read Position Rank Sum Test.
|See the Technical Documentation for Homopolymer Run.
|See the Technical Documentation for Haplotype Score.
|See the Technical Documentation for Qual By Depth.
|Only present when using Variant quality score recalibration. Log odds ratio of being a true variant versus being false under the trained gaussian mixture model.
|See the Technical Documentation for Fisher Strand
|How much evidence is there for Strand Bias (the variation being seen on only the forward or only the reverse strand) in the reads? Higher SB values denote more bias (and therefore are more likely to indicate false positive calls).
Our testing has shown that not all combinations of snpEff/database versions produce high-quality results. Be sure to read this document completely to familiarize yourself with our recommended best practices BEFORE running snpEff.
Until recently we were using an in-house annotation tool for genomic annotation, but the burden of keeping the database current and our lack of ability to annotate indels has led us to employ the use of a third-party tool instead. After reviewing many external tools (including annoVar, VAT, and Oncotator), we decided that SnpEff best meets our needs as it accepts VCF files as input, can annotate a full exome callset (including indels) in seconds, and provides continually-updated transcript databases. We have implemented support in the GATK for parsing the output from the SnpEff tool and annotating VCFs with the information provided in it.
Download the SnpEff core program. If you want to be able to run VariantAnnotator on the SnpEff output, you'll need to download a version of SnpEff that VariantAnnotator supports from this page (currently supported versions are listed below). If you just want the most recent version of SnpEff and don't plan to run VariantAnnotator on its output, you can get it from here.
After unzipping the core program, open the file snpEff.config in a text editor, and change the "database_repository" line to the following:
database_repository = http://sourceforge.net/projects/snpeff/files/databases/
Then, download one or more databases using SnpEff's built-in download command:
java -jar snpEff.jar download GRCh37.64
You can find a list of available databases here. The human genome databases have GRCh or hg in their names. You can also download the databases directly from the SnpEff website, if you prefer.
The download command by default puts the databases into a subdirectory called data within the directory containing the SnpEff jar file. If you want the databases in a different directory, you'll need to edit the
data_dir entry in the file
snpEff.config to point to the correct directory.
Run SnpEff on the file containing your variants, and redirect its output to a file. SnpEff supports many input file formats including VCF 4.1, BED, and SAM pileup. Full details and command-line options can be found on the SnpEff home page.
If you want to take advantage of SnpEff integration in the GATK, you'll need to run SnpEff version **2.0.5*. Note: newer versions are currently unsupported by the GATK, as we haven't yet had the reources to test it.
These best practices are based on our analysis of various snpEff/database versions as described in detail in the Analysis of SnpEff Annotations Across Versions section below.
We recommend using only the GRCh37.64 database with SnpEff 2.0.5. The more recent GRCh37.65 database produces many false-positive Missense annotations due to a regression in the ENSEMBL Release 65 GTF file used to build the database. This regression has been acknowledged by ENSEMBL and is supposedly fixed as of 1-30-2012; however as we have not yet tested the fixed version of the database we continue to recommend using only GRCh37.64 for now.
We recommend always running with
-onlyCoding true with human databases (eg., the GRCh37.* databases). Setting
-onlyCoding false causes snpEff to report all transcripts as if they were coding (even if they're not), which can lead to nonsensical results. The
-onlyCoding false option should only be used with databases that lack protein coding information.
Do not trust annotations from versions of snpEff prior to 2.0.4. Older versions of snpEff (such as 2.0.2) produced many incorrect annotations due to the presence of a certain number of nonsensical transcripts in the underlying ENSEMBL databases. Newer versions of snpEff filter out such transcripts.
See our analysis of the SNP annotations produced by snpEff across various snpEff/database versions here.
Both snpEff 2.0.2 + GRCh37.63 and snpEff 2.0.5 + GRCh37.65 produce an abnormally high Missense:Silent ratio, with elevated levels of Missense mutations across the entire spectrum of allele counts. They also have a relatively low (~70%) level of concordance with the 1000G Gencode annotations when it comes to Silent mutations. This suggests that these combinations of snpEff/database versions incorrectly annotate many Silent mutations as Missense.
snpEff 2.0.4 RC3 + GRCh37.64 and snpEff 2.0.5 + GRCh37.64 produce a Missense:Silent ratio in line with expectations, and have a very high (~97%-99%) level of concordance with the 1000G Gencode annotations across all categories.
See our comparison of SNP annotations produced using the GRCh37.64 and GRCh37.65 databases with snpEff 2.0.5 here
The GRCh37.64 database gives good results on the condition that you run snpEff with the
-onlyCoding true option. The
-onlyCoding false option causes snpEff to mark all transcripts as coding, and so produces many false-positive Missense annotations.
The GRCh37.65 database gives results that are as poor as those you get with the
-onlyCoding false option on the GRCh37.64 database. This is due to a regression in the ENSEMBL release 65 GTF file used to build snpEff's GRCh37.65 database. The regression has been acknowledged by ENSEMBL and is due to be fixed shortly.
See our analysis of the INDEL annotations produced by snpEff across snpEff/database versions here
Below is an example of how to run SnpEff version 2.0.5 with a VCF input file and have it write its output in VCF format as well. Notice that you need to explicitly specify the database you want to use (in this case, GRCh37.64). This database must be present in a directory of the same name within the
data_dir as defined in
java -Xmx4G -jar snpEff.jar eff -v -onlyCoding true -i vcf -o vcf GRCh37.64 1000G.exomes.vcf > snpEff_output.vcf
In this mode, SnpEff aggregates all effects associated with each variant record together into a single INFO field annotation with the key EFF. The general format is:
EFF=Effect1(Information about Effect1),Effect2(Information about Effect2),etc.
And here is the precise layout with all the subfields:
It's also possible to get SnpEff to output in a (non-VCF) text format with one Effect per line. See the SnpEff home page for full details.
Once you have a SnpEff output VCF file, you can use the VariantAnnotator walker to add SnpEff annotations based on that output to the input file you ran SnpEff on.
There are two different options for doing this:
NOTE: This option works only with supported SnpEff versions as explained above. VariantAnnotator run as described below will refuse to parse SnpEff output files produced by other versions of the tool, or which lack a SnpEff version number in their header.
The default behavior when you run VariantAnnotator on a SnpEff output file is to parse the complete set of effects resulting from the current variant, select the most biologically-significant effect, and add annotations for just that effect to the INFO field of the VCF record for the current variant. This is the mode we plan to use in our Production Data-Processing Pipeline.
When selecting the most biologically-significant effect associated with the current variant, VariantAnnotator does the following:
Prioritizes the effects according to the categories (in order of decreasing precedence) "High-Impact", "Moderate-Impact", "Low-Impact", and "Modifier", and always selects one of the effects from the highest-priority category. For example, if there are three moderate-impact effects and two high-impact effects resulting from the current variant, the annotator will choose one of the high-impact effects and add annotations based on it. See below for a full list of the effects arranged by category.
Within each category, ties are broken using the functional class of each effect (in order of precedence: NONSENSE, MISSENSE, SILENT, or NONE). For example, if there is both a NON_SYNONYMOUS_CODING (MODERATE-impact, MISSENSE) and a CODON_CHANGE (MODERATE-impact, NONE) effect associated with the current variant, the annotator will select the NON_SYNONYMOUS_CODING effect. This is to allow for more accurate counts of the total number of sites with NONSENSE/MISSENSE/SILENT mutations. See below for a description of the functional classes SnpEff associates with the various effects.
Effects that are within a non-coding region are always considered lower-impact than effects that are within a coding region.
Example Usage:
java -jar dist/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R /humgen/1kg/reference/human_g1k_v37.fasta \
-A SnpEff \
--variant 1000G.exomes.vcf \ (file to annotate)
--snpEffFile snpEff_output.vcf \ (SnpEff VCF output file generated by running SnpEff on the file to annotate)
-L 1000G.exomes.vcf \
-o out.vcf
VariantAnnotator adds some or all of the following INFO field annotations to each variant record:
SNPEFF_EFFECT - The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)
SNPEFF_IMPACT - Impact of the highest-impact effect resulting from the current variant (
LOW, or
SNPEFF_FUNCTIONAL_CLASS - Functional class of the highest-impact effect resulting from the current variant (
MISSENSE, or
SNPEFF_CODON_CHANGE - Old/New codon for the highest-impact effect resulting from the current variant
SNPEFF_AMINO_ACID_CHANGE - Old/New amino acid for the highest-impact effect resulting from the current variant
SNPEFF_GENE_NAME - Gene name for the highest-impact effect resulting from the current variant
SNPEFF_GENE_BIOTYPE - Gene biotype for the highest-impact effect resulting from the current variant
SNPEFF_TRANSCRIPT_ID - Transcript ID for the highest-impact effect resulting from the current variant
SNPEFF_EXON_ID - Exon ID for the highest-impact effect resulting from the current variant
Example VCF records annotated using SnpEff and VariantAnnotator:
1 874779 . C T 279.94 . AC=1;AF=0.0032;AN=310;BaseQRankSum=-1.800;DP=3371;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4493;InbreedingCoeff=-0.0045;
1 874816 . C CT 2527.52 . AC=15;AF=0.0484;AN=310;BaseQRankSum=-11.876;DP=4718;FS=48.575;HRun=1;HaplotypeScore=91.9147;InbreedingCoeff=-0.0520;
VariantAnnotator also has the ability to take the EFF field from the SnpEff VCF output file containing all the effects aggregated together and copy it verbatim into the VCF to annotate.
Here's an example of how to do this:
java -jar dist/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R /humgen/1kg/reference/human_g1k_v37.fasta \
-E resource.EFF \
--variant 1000G.exomes.vcf \ (file to annotate)
--resource snpEff_output.vcf \ (SnpEff VCF output file generated by running SnpEff on the file to annotate)
-L 1000G.exomes.vcf \
-o out.vcf
Of course, in this case you can also use the VCF output by SnpEff directly, but if you are using VariantAnnotator for other purposes anyway the above might be useful.
Below are the possible genomic effects recognized by SnpEff, grouped by biological impact. Full descriptions of each effect are available on this page.
SnpEff assigns a functional class to certain effects, in addition to an impact:
NONSENSE: assigned to point mutations that result in the creation of a new stop codon
MISSENSE: assigned to point mutations that result in an amino acid change, but not a new stop codon
SILENT: assigned to point mutations that result in a codon change, but not an amino acid change or new stop codon
NONE: assigned to all effects that don't fall into any of the above categories (including all events larger than a point mutation)
The GATK prioritizes effects with functional classes over effects of equal impact that lack a functional class when selecting the most significant effect in VariantAnnotator. This is to enable accurate counts of NONSENSE/MISSENSE/SILENT sites.
2 SNPs with significant strand bias
Several SNPs with excessive coverage
For a complete, detailed argument reference, refer to the GATK document page here.
In addition to true variation, variant callers emit a number of false-positives. Some of these false-positives can be detected and rejected by various statistical tests. VariantAnnotator provides a way of annotating variant calls as preparation for executing these tests.
Description of the haplotype score annotation
The list below is not comprehensive. Please use the
--list argument to get a list of all possible annotations available. Also, see the FAQ article on understanding the Unified Genotyper's VCF files for a description of some of the more standard annotations.
Note that technically the VariantAnnotator does not require reads (from a BAM file) to run; if no reads are provided, only those Annotations which don't use reads (e.g. Chromosome Counts) will be added. But most Annotations do require reads. When running the tool we recommend that you add the
-L argument with the variant rod to your command line for efficiency and speed.


text:
Rushville Republican
---- — Three hundred seventy-three Rush County residents benefited from The Salvation Army's Emergency Assistance program in 2012. More than $6,500 in direct financial assistance was distributed to Rush County residents who needed help meeting their basic needs.
The Emergency Assistance program is largely supported by the Rush County United Fund and helps to ensure that there is always a place within the county for people with basic and immediate human needs to seek support.
Through its Emergency Assistance Program, The Salvation Army helps residents who are unable to afford their utility bills, transportation expenses related to medical appointments and employment, groceries, clothing, housing expenses and other necessary expenses.
With the slow rebound of the economy, this type of basic needs service remains extremely important.
In addition to the Emergency Assistance program, The Salvation Army also provides several other important services within the community.
The Salvation Army assists nursing home residents during the Christmas and Easter holiday seasons through its League of Mercy program. Last year, the program served 177 seniors in the county.
The Salvation Army's Disaster Services team is ready and willing to respond if needed in the event of a major disaster, such as a tornado or flooding, in the community.
The Salvation Army is proud to receive support from the Rush County United Fund and asks all residents to give generously to the United Fund campaign.
For more about the Service Extension program and other programs and services conducted within Indiana, visit The Salvation Army online at www.salvationarmyindiana.org.
— Rushville Republican


text:
(from the manuscript "In My Grasp")
He'd asked why I wore cornrows to school.
So I began to wish that the Crème of Nature bottle
would transform my Afro into a flawless, vibrant canopy.
Long hair would make me pretty, I was sure of it
the chemicals weren't good enough.
And when a short, skinny, light-skinned local train would
flutter by
his eyes would follow her into ether,
and I thought that mine weren't light enough.
He turned me off
going to school with a drawstring bag that cradled only
an unsharpened pencil.
He forgot things that took so much courage
for me to tell,
and he had the ability to make me question myself
when he barely had the ability to read.
But he turned me on
when I hugged him, I touched cloud 546,999
feeling like I'd digested butterflies
and I was glad that there was something in me
somebody else liked.
My affection has withered away and died
like the smoke rings between his parched lips.
On tomorrow's tomorrow I will wake up for school
tired and groggy with stress.
There will be rows and rows of braids in my hair,
and I will deflate under the weight of my book bag
ripping at the stitches because of my books.
I'll embrace the sun as my skin gets darker
I won't hold onto my Colorblends as tightly
and I will let my hopes of being stereotypically attractive fade.
Because I'm finally over him.
This piece has been published in Teen Ink's monthly print magazine.


text:
FIRE 154 - Wildland Urban Interface Operations (3)
- Prerequisite: "C" or higher in ENG 22/60 or ESL 23, OR Placement in ENG 100; Placement in MATH 24/50
This course is an introduction to the strategies, tactics, techniques, tools and safety consideration related to fire operations in the wildland/urban interface. The course involves aspects of suppression and prevention.
3 hrs. lect. per week
Student Learning Outcomes
Upon successful completion of FIRE 154, the student will be able to:
- List those items that should be included in a size-up report; to be considered in sizing-up an interface fire incident prior to and after arriving at the scene; and evaluating the types and limitations of resources needed
- List the three priorities when establishing strategic goals and three operational modes
- List five items which would influence your resource order, and four subject areas to consider when briefing and deploying your resources
- Identify the three structure triage categories, and five basic factors upon which you base your triage decisions, and four conditions that may mean the situation is hopeless
- Identify four operations you should accomplish upon your arrival at the incident or assigned area, and describe their importance to your firefighting actions
- Describe how to prepare structures and the surrounding area to minimize damage, and firefighting methods employed to defend threatened structures from fire
- List the items that need to be considered in assessing the effectiveness of an action plan, and demonstrate your ability to properly update the action plan when the scenario changes
- List several steps that should be completed before leaving an area involved in an interface fire
- Identify several important factors in dealing with the public at an interface fire, and the importance of an organized demobilization plan
- Describe how you can minimize and protect against damage to public and private property
- Describe 12 general safety considerations often encountered in interface operations
- List the structural situations that shout "Watch Out" and seven don't when working around power lines
- Accreditation
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