text:
A new tool has been released!
Check out the documentation at CombineVariants.
This tool combines VCF records from different sources. Any (unique) name can be used to bind your rod data and any number of sources can be input. This tool currently supports two different combination types for each of variants (the first 8 fields of the VCF) and genotypes (the rest)
For a complete, detailed argument reference, refer to the GATK document page here.
CombineVariants will include a record at every site in all of your input VCF files, and annotate which input ROD bindings the record is present, pass, or filtered in in the set attribute in the
INFO field (see below). In effect, CombineVariants always produces a union of the input VCFs. However, any part of the Venn of the N merged VCFs can be exacted using JEXL expressions on the set attribute using SelectVariants. If you want to extract just the records in common between two VCFs, you would first CombineVariants the two files into a single VCF, and then run SelectVariants to extract the common records with
-select 'set == "Intersection"', as worked out in the detailed example below.
-filteredRecordsMergeType argument determines how CombineVariants handles sites where a record is present in multiple VCFs, but it is filtered in some and unfiltered in others, as described in the Tech Doc page for the tool.
The set
INFO field indicates which call set the variant was found in. It can take on a variety of values indicating the exact nature of the overlap between the call sets. Note that the values are generalized for multi-way combinations, but here we describe only the values for 2 call sets being combined.
set=Intersection : occurred in both call sets, not filtered out
set=NAME : occurred in the call set
NAME only
set=NAME1-filteredInNAME : occurred in both call sets, but was not filtered in
NAME1 but was filtered in
set=filteredInAll : occurred in both call sets, but was filtered out of both
For three or more call sets combinations, you can see records like
NAME1-NAME2 indicating a variant occurred in both
NAME1 and
NAME2 but not all sets.
You can use
-setKey foo to change the
set=XXX tag to
foo=XXX in your output. Additionally, -
setKey null stops the set tag=value pair from being emitted at all.
Add the
-minimalVCF argument to CombineVariants if you want to eliminate unnecessary information from the
INFO field and genotypes. The only fields emitted will be
GT:GQ for genotypes and the
keySet for
An even more extreme output format is
-sites_only, a general engine capability, where the genotypes for all samples are completely stripped away from the output format. Enabling this option results in a significant performance speedup as well.
Add the
-minN (or
--minimumN) command, followed by an integer if you want to only output records present in at least N input files. Useful, for example in combining several data sets where we only want to keep sites present in for example at least 2 of them (in which case
-minN 2 should be added to the command line).
In the following example, we use CombineVariants and SelectVariants to obtain only the sites in common between the OMNI 2.5M and HapMap3 sites in the GSA bundle.
java -Xmx2g -jar dist/GenomeAnalysisTK.jar -T CombineVariants -R bundle/b37/human_g1k_v37.fasta -L 1:1-1,000,000 -V:omni bundle/b37/1000G_omni2.5.b37.sites.vcf -V:hm3 bundle/b37/hapmap_3.3.b37.sites.vcf -o union.vcf
java -Xmx2g -jar dist/GenomeAnalysisTK.jar -T SelectVariants -R ~/Desktop/broadLocal/localData/human_g1k_v37.fasta -L 1:1-1,000,000 -V:variant union.vcf -select 'set == "Intersection";' -o intersect.vcf
This results in two vcf files, which look like:
==> union.vcf <==
1 990839 SNP1-980702 C T . PASS AC=150;AF=0.05384;AN=2786;CR=100.0;GentrainScore=0.7267;HW=0.0027632264;set=Intersection
1 990882 SNP1-980745 C T . PASS CR=99.79873;GentrainScore=0.7403;HW=0.005225421;set=omni
1 990984 SNP1-980847 G A . PASS CR=99.76005;GentrainScore=0.8406;HW=0.26163524;set=omni
1 992265 SNP1-982128 C T . PASS CR=100.0;GentrainScore=0.7412;HW=0.0025895447;set=omni
1 992819 SNP1-982682 G A . id50 CR=99.72961;GentrainScore=0.8505;HW=4.811053E-17;set=FilteredInAll
1 993987 SNP1-983850 T C . PASS CR=99.85935;GentrainScore=0.8336;HW=9.959717E-28;set=omni
1 994391 rs2488991 G T . PASS AC=1936;AF=0.69341;AN=2792;CR=99.89378;GentrainScore=0.7330;HW=1.1741E-41;set=filterInomni-hm3
1 996184 SNP1-986047 G A . PASS CR=99.932205;GentrainScore=0.8216;HW=3.8830226E-6;set=omni
1 998395 rs7526076 A G . PASS AC=2234;AF=0.80187;AN=2786;CR=100.0;GentrainScore=0.8758;HW=0.67373306;set=Intersection
1 999649 SNP1-989512 G A . PASS CR=99.93262;GentrainScore=0.7965;HW=4.9767335E-4;set=omni
==> intersect.vcf <==
1 950243 SNP1-940106 A C . PASS AC=826;AF=0.29993;AN=2754;CR=97.341675;GentrainScore=0.7311;HW=0.15148845;set=Intersection
1 957640 rs6657048 C T . PASS AC=127;AF=0.04552;AN=2790;CR=99.86667;GentrainScore=0.6806;HW=2.286109E-4;set=Intersection
1 959842 rs2710888 C T . PASS AC=654;AF=0.23559;AN=2776;CR=99.849;GentrainScore=0.8072;HW=0.17526293;set=Intersection
1 977780 rs2710875 C T . PASS AC=1989;AF=0.71341;AN=2788;CR=99.89077;GentrainScore=0.7875;HW=2.9912625E-32;set=Intersection
1 985900 SNP1-975763 C T . PASS AC=182;AF=0.06528;AN=2788;CR=99.79926;GentrainScore=0.8374;HW=0.017794203;set=Intersection
1 987200 SNP1-977063 C T . PASS AC=1956;AF=0.70007;AN=2794;CR=99.45917;GentrainScore=0.7914;HW=1.413E-42;set=Intersection
1 987670 SNP1-977533 T G . PASS AC=2485;AF=0.89196;AN=2786;CR=99.51427;GentrainScore=0.7005;HW=0.24214932;set=Intersection
1 990417 rs2465136 T C . PASS AC=1113;AF=0.40007;AN=2782;CR=99.7599;GentrainScore=0.8750;HW=8.595538E-5;set=Intersection
1 990839 SNP1-980702 C T . PASS AC=150;AF=0.05384;AN=2786;CR=100.0;GentrainScore=0.7267;HW=0.0027632264;set=Intersection
1 998395 rs7526076 A G . PASS AC=2234;AF=0.80187;AN=2786;CR=100.0;GentrainScore=0.8758;HW=0.67373306;set=Intersection
GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Note that this release is relatively smaller than previous ones. We are working hard on some new tools and frameworks that we are hoping to make available to everyone for our next release.
GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Currently I am following GATK best practice for using HC 3.0+, however I'm splitting my calls to chromosomal regions (-L). Next are the following step I perform working up to GenotypeGVCF and my question.
1 - I use CatVariants (following HC) to merge all 25 chromosome gvcf files into a single gvcf file per individual.
2 - I use CombineGVCF to merge 2 .. n number of individuals together. This is done because some analysis have 300+ individuals. 3- I then use CombineGVCF again to merge all the file from step 2 into one large gvcf file for one large joint GenotypeGVCF step. 4 - GenotypeGVCF is done again based on chromosomal regions (-L), which is followed by a additional CatVariants before VQSR.
The question I have this this: Given the size of the analysis I have noticed that my CombineGVCF done in step 3 can take anywhere from 4-8 hours. I was wondering if I could change this step to use CombineVariants and have the result be the same (unlost data). The main reason for this would be because GATK currently allow CombineVariants to use the -nt option.
Thanks for you time and work.
Is there a page, where I can see an example of what CombineVariants does with and without --printComplexMerges? I'm wondering whether to use bcftools merge or GATK CombineVariants.
Dear GATK team,
I am running the following command:
java -jar GenomeAnalysisTK_v33.jar -R genome.fa -T CombineVariants --variant file1.vcf --variant file2.vcf --variant file3.vcf --variant file4.vcf --variant file5.vcf --variant file6.vcf --variant file7.vcf --variant file8.vcf --variant file9.vcf --variant file10.vcf --minimumN 10 -o combined.vcf -genotypeMergeOptions UNIQUIFY
The output vcf file has the header for the sample columns:
sample.variant sample.variant10 sample.variant2 sample.variant3 sample.variant4 sample.variant5 sample.variant6 sample.variant7 sample.variant8 sample.variant9
What do these numbers represent? For example, does sample.variant10 equal to the 10th VCF file (it would be file10.vcf in this case) and so on?
Thank you!
Hey GATK Team!
I'm attempting to merge identical sample sets called on different (disjoint) chromosomes with the
CombineVariants tool with the
--assumeIdenticalSamples flag enabled, but the v3.3-0 tool is behaving as if this option is not enabled and it requests I specify a
--genotypemergeoption. When I execute the same exact command using v3.2-2, the tool runs to completion without error.
--genotypemergeoption UNIQIFY with v3.3-0 just to see what happens (while
--assumeIdenticalSamples is still enabled) outputs each sample 18 times (once for each chromosome) without any loss in the number of loci (sum of loci in individual files equals sum in combined output file).
I believe this may be a bug, but I could be wrong...
INFO 13:10:49,188 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:10:49,190 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 13:10:49,191 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:10:49,191 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:10:49,194 HelpFormatter - Program Args: -T CombineVariants -R genome.fasta -V ./homVar.list --out homVar.SNP.vcf --suppressCommandLineHeader --assumeIdenticalSamples
INFO 13:10:49,198 HelpFormatter - Executing as firstname.lastname@example.com on Linux 2.6.32-431.20.3.el6.nersc.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13.
INFO 13:10:49,198 HelpFormatter - Date/Time: 2014/12/28 13:10:49
INFO 13:10:49,199 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:10:49,199 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:10:49,731 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:10:50,015 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:10:50,731 GenomeAnalysisEngine - Preparing for traversal
INFO 13:10:50,751 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:10:50,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:10:50,752 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:10:50,752 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 13:10:51,578 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
##### 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: Duplicate sample names were discovered but no genotypemergeoption was supplied. To combine samples without merging specify --genotypemergeoption UNIQUIFY. Merging duplicate samples without specified priority is unsupported, but can be achieved by specifying --genotypemergeoption UNSORTED.
INFO 13:02:06,270 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:02:06,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 13:02:06,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:02:06,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:02:06,275 HelpFormatter - Program Args: -T CombineVariants -R genome.fasta -V ./homVar.list --out homVar.SNP.vcf --suppressCommandLineHeader --assumeIdenticalSamples
INFO 13:02:06,279 HelpFormatter - Executing as firstname.lastname@example.com on Linux 2.6.32-431.20.3.el6.nersc.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13.
INFO 13:02:06,280 HelpFormatter - Date/Time: 2014/12/28 13:02:06
INFO 13:02:06,280 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:02:06,280 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:02:06,812 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:02:07,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:02:07,818 GenomeAnalysisEngine - Preparing for traversal
INFO 13:02:07,837 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:02:07,838 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:02:07,838 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:02:07,838 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 13:02:07,840 CombineVariants - Priority string is not provided, using arbitrary genotyping order: null
INFO 13:02:10,798 ProgressMeter - done 2967.0 2.0 s 16.6 m 88.9% 2.0 s 0.0 s
INFO 13:02:10,799 ProgressMeter - Total runtime 2.96 secs, 0.05 min, 0.00 hours
INFO 13:02:11,589 GATKRunReport - Uploaded run statistics report to AWS S3
Hi GATK team,
I am attempting to combine a HaplotypeCaller generated VCF with some indels called using pindel using the following arguments (GATK v3.3-0-g37228af):
-R /data/shared/ref/b37/human_g1k_v37.fasta -T CombineVariants --variant:GATK var.HiSeqDecember.raw.vcf --variant:pindel pindel_combined.vcf -o var.HiSeqDecember.pindel.raw.vcf -genotypeMergeOptions PRIORITIZE -priority GATK,pindel
However I get the following error:
ERROR MESSAGE: Badly formed variant context at location 1:157718231; getEnd() was 157718235 but this VariantContext contains an END key with value 157718231
The variants in question are (from GATK):
1 157718231 . CAAAT C,CAAATAAAT 2533.56 PASS AC=3,13;AF=0.125,0.542;AN=24;BaseQRankSum=1.762;ClippingRankSum=-0.327;DP=126;FS=0.000;HOMLEN=39;HOMSEQ=AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA;InbreedingCoeff=-0.1260;MLEAC=3,13;MLEAF=0.125,0.542;MQ=70.00;MQ0=0;MQRankSum=0.920;QD=22.22;ReadPosRankSum=-0.893;SOR=0.976;SVLEN=4;SVTYPE=INS;set=Intersection GT:DP:GQ 0/0:10:30 0/2:9:18 2/2:6:18 2/2:5:15 0/1:10:99 0/2:14:99 2/2:8:24 2/2:6:18 2/2:7:21 0/2:17:99 0/1:5:75 0/1:6:27
and (from pindel):
1 157718231 . C CAAAT . PASS AC=2;AF=0.143;AN=14;END=157718231;HOMLEN=39;HOMSEQ=AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA;SVLEN=4;SVTYPE=INS;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10 GT:AD ./. ./. 0/0:0,7 0/0:0,6 ./. 0/0:0,9 0/0:0,8 0/0:0,7 0/0:0,8 1/1:0,12 ./. ./.
It is worth noting that the pindel VCF here was merged together from several pindel-generated VCFs using CombineVariants without any complaint from the GATK. It looks to me that the END key is correct for the pindel variant (a simple insertion), but the GATK is confused due to the mixed deletion/insertion variant generated by the HaplotypeCaller at the same position (without an END key).
I can rerun the command after stripping all END tags from the pindel VCF and the command completes successfully, so this is not a showstopper for me but I assume this is a bug(?) and if so, it would be great if there were a fix.
Hi GATK team, i would like to seek opinion from your team to find the best workflow that best fit my data. Previously i've been exploring both variant calling algorithms UnifiedGenotyper and HaplotypeCaller, and i would love to go for UnifiedGenotyper considering of the sensitivity and the analysis runtime. Due to my experimental cohort samples grows from time to time, so i've opt for single sample calling follow by joint-analysis using combineVariants instead of doing multiple-samples variant calling. However by doing so, i've experience few drawbacks from it (this issue was discussed at few forums). For a particular SNP loci, we wouldn't know whether the "./." reported for some of the samples are due to no reads covering that particular loci, or it doesn't pass certain criteria during variant calling performed previously, or it is a homo-reference base (which i concern this most and can't cope to lost this information).
Then, i found this "gvcf", and it is potentially to solve my problem (Thanks GATK team for always understand our researcher's need)!! Again, i'm insist of opt for unifiedGenotyper instead of haplotypeCaller to generate the gvcf, and reading from the forum at https://www.broadinstitute.org/gatk/guide/tagged?tag=gvcf, i would assume that as VCFs produced by "UnifiedGenotyper with --output_mode EMIT_ALL_SITES" to be something alike with the gvcf file produced by HaplotyperCaller. However i couldn't joint them up using either "CombineVariants" or "CombineGVCFs", most probably i think "UnifiedGenotyper with --output_mode EMIT_ALL_SITES" doesn't generate gvcf format.
Can you please give me some advice to BEST fit my need and with minimum runtime (UnifiedGenotyper would be my best choice), is there any method to joint the ALL_SITES vcf file produced by UnifiedGenotyper which i might probably missed out from the GATK page?
Hello everyone, I recenltly ran -T CombineVariants on a set of samples and I noticed that the allele frequency (AF) in the info field changed. In the individual VCF, AF=0.3 for the particular variant I was looking at, however, after I combined multiple VCFs, AF=0.5.... however the variant was only seen in the one sample, so how could the frequency change? Any insight is appreciated.
Thank you,
I am merging several genome vcf files apparently created by gvcftools [1]. I noticed that CombineVariants is incorrectly summing allele counts (AC) in some corner cases, and was wondering if the format [2] was supported?
If the format should be supported by the CombineVariants tool (gvcf is VCF 4.1 conformant), I have isolated a minimal example that should be of help for bugfixing.
[1] https://sites.google.com/site/gvcftools/home [2] https://sites.google.com/site/gvcftools/home/about-gvcf
Thanks, Paweł
Hi GATK team,
I was working on generating a combined VCF using 150+ VCFs (building the sort of cohort). The purpose of it is to calculate variants cohort frequency. But I found the genotype is messed up in the combined VCF. Here is my cmd line:
java -jar /GATK/GenomeAnalysisTK-2.7-4/GenomeAnalysisTK.jar -R refernce.fasta \
-T CombineVariants \
--variant sample1.vcf \
--variant sample2.vcf \
-o combined.vcf
Here is one example of one variant/ position in the combined VCF. The record is very long in the combined VCF, I just grabbed the related columns here.
1 22082967 rs35545280 CAAA CAA,C,CA,CAAAA 76.73 PASS AC=109,6,104,6;AF=0.368,0.020,0.351,0.020;AN=296;DB;DP=9869;GC=48.13;MQ0=0;PercentNBaseSolid=0.0000;RU=A;STR;set=filterInvariant-filterInvariant2-filterInvariant3… GT:DP:GQ
In this record, sample 1 has this variant and it shows as "0/3:46:99",
but in the sample1.vcf, it is listed as
1 22082967 rs35545280 CA C 88.73 Low_Confidence AC=2;AF=1.00;AN=2;BaseCounts=0,76,0,0;BaseQRankSum=1.905;DB;DP=76;FS=0.000;GC=48.13;HaplotypeScore=195.0572;IndelType=DEL.NOVEL_2.;LowMQ=0.0000,0.0000,76;MLEAC=1;MLEAF=0.500;MQ=68.40;MQ0=0;MQRankSum=0.423;PercentNBaseSolid=0.0000;QD=1.17;RPA=20,19;RU=A;ReadPosRankSum=-0.741;STR;set=FilteredInAll GT:AD:DP:GQ:PL 1/1:0,17:76:19:587,19,0
And you can see that the genotype in combined VCF for sample 1 is 0/3, but in its original its is 1/1 which is homozygous. So when I calculate the cohort frequency, I'm confused on matching genotype of this variant for sample 1.
To give you more idea, I listed another sample of same variant in combined.VCF and its record in sample2.VCF.
In the combined.VCF, sample 2 shows as "0/3:91:99".
In the sample2.VCF, the record is:
1 22082967 rs35545280 CAA C,CA 549.19 PASS AC=1,1;AF=0.500,0.500;AN=2;BaseCounts=0,105,0,0;BaseQRankSum=-1.897;DB;DP=105;FS=0.000;GC=48.13;HaplotypeScore=238.8742;IndelType=MULTIALLELIC_INDEL;LowMQ=0.0000,0.0000,105;MLEAC=1,1;MLEAF=0.500,0.500;MQ=68.78;MQ0=0;MQRankSum=-0.992;PercentNBaseSolid=0.0000;QD=5.23;RPA=20,18,19;RU=A;ReadPosRankSum=-1.344;STR;set=variant2 GT:AD:DP:GQ:PL 1/2:0,11,25:105:99:1363,307,775,501,0,585
Where you can see the genotype is 1/2, but in the combined VCF, it shows as "0/3".
Please advise me if I should use any parameter in the cmd line to solve this problem.
Thank you. Linda
Hi all, I have a minor concern.
After using CombineVariants tools to combine variants from GATK and Samtools, MQ annotation is missing for some of the variants specifically for variants which are present in both GATK and Samtools. Below is an example:
$grep "16203159" VCF/GatkSNP.vcf
chr8 16203159 . G T 4609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.105;ClippingRankSum=0.652;DP=333;
$ grep "16203159" VCF/SamSNP.vcf
chr8 16203159 . G T 225 . DP=346;VDB=4.969420e-01;RPB=-1.470555e+00;AF1=0.5;AC1=1;DP4=82,84,81,92;
MQ=58;FQ=225;PV4=0.66,6.2e-09,1,1 GT:PL:GQ 0/1:255,0,255:99
MQ annotation is present in both the VCF files. But after combining MQ is missing as shown below:
$ grep "16203159" TMP_files/SNP_INDEL.vcf
chr8 16203159 . G T 4609.77 . AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=-7.105;
Variants which are present in only of the VCF files do have MQ annotation after using CombineVariants. This happens only for variants which are present in both VCF files. Could you help to get MQ annotations in this case?
Here is the command used:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fa --variant:GatkSNP GatkSNP.vcf --variant:GatkINDEl GatkINDEL.vcf
--variant:SamSNP SamSNP.vcf --variant:SamINDEL SamINDEL.vcf -o SNP_INDEL.vcf -genotypeMergeOptions PRIORITIZE -priority
GatkSNP,GatkINDEL,SamSNP,SamINDEL --filteredrecordsmergetype KEEP_UNCONDITIONAL
Hello everyone, I have used the ion proton system to sequence 15 sample exomes so far. In this system, only 3 samples can be run at a given time, so I essentially have five sets of samples. Is it still possible to use CombineVariants on the VCF files of samples that were from different sequencing runs? Thank you, Ricky
I have used CombineVariants to combine variants from GATK and samtools as shown below:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fa --variant:GatkSNP GATKsnp.vcf --variant:GatkINDEL GATKind.vcf --variant:SamSNP Samsnp.vcf --variant:SamINDEL Samind.vcf -o allvar.vcf -genotypeMergeOptions PRIORITIZE -priority GatkSNP,GatkINDEL,SamSNP,SamINDEL --filteredrecordsmergetype KEEP_UNCONDITIONAL
This merges all the variants. However, with the above command, i do get the variants present in both GATK and samtools emitted from samtools.
I would like to get all the variants such that:
could someone suggest any ideas or of there is something to be fixed in the command.
I am running CombineVariants followed by VariantEval on two VCF files (GATK version 3.1-1). I noticed that none of my "set=FilteredInAll" variants are included in the output of VariantEval. I suspect this is because the FILTER column is not "PASS" because the variants were not "PASS" in either of the input VCF files.
Is there an argument to pass into VariantEval so that it does not filter variants out based on the FILTER column? I was using the arguments from a guide article (http://gatkforums.broadinstitute.org/discussion/48/using-varianteval). I saw that in the comments you mentioned an --ignoreFilters argument, but when I tried to use it I got the GATK error: Argument with name 'ignoreFilters' isn't defined.
I can just change the FILTER column entries in the combined VCF file, but it seems like a problem that others might have as well.
Thank you!
Hi I have two vcf files, each with the same chr:pos, but alleles are different:
$ tail -1 test1.snp.vcf chr17 41267926 . G A 50.77 . xxx GT:AD:DP:GQ:P 0/1:2,3:6:49:79,0,49 $ tail -1 test2.snp.vcf chr17 41267926 . G C 15.88 LowQual xxx GT:AD:DP:GQ:P 0/1:3,2:6:44:44,0,85
After running CombineVariants below
$ java -jar GenomeAnalysisTK.jar -T CombineVariants -R ucsc.hg19.fasta -V test1.snp.vcf -V test2.snp.vcf -o ThreeAlleles.snp.vcf -genotypeMergeOptions UNIQUIFY
The ThreeAlleles.snp.vcf only have GT:DP:GQ instead of GT:AD:DP:GQ:PL in the FORMAT field
$ tail -1 ThreeAlleles.snp.vcf chr17 41267926 . G A,C 50.77 PASS xxx GT:DP:GQ 0/1:6:49 0/2:6:44
How can I retain the GT:AD:DP:GQ:PL format for tri-allelic positions?
I was wondering if there is a method for filtering individual genotype calls when using CombineVariants to merge single-called VCF files. The desired behavior that I would like would be a hybrid between the KEEP_IF_ANY_UNFILTERED and KEEP_IF_ALL_UNFILTERED arguments to the -filteredRecordsMergeType. By this, I mean that any site that is unfiltered in any input will remain unfiltered in the output, but for any genotype call from a filtered input should have a filter annotation in the "FT" field of the genotype. I will show a simplified example below (extraneous columns removed from the sample files):
Input 1:
#CHROM POS ID (...) FILTER FORMAT SAMPLE1 1 11916764 rs79387574 (...) PASS GT:DP 0/0:45
Input 2:
#CHROM POS ID (...) FILTER FORMAT SAMPLE2 1 11916764 rs79387574 (...) LowQ GT:DP 0/1:3
Desired Output:
#CHROM POS ID (...) FILTER FORMAT SAMPLE1 SAMPLE2 1 11916764 rs79387574 (...) PASS GT:DP:FT 0/0:45:PASS 0/1:3:LowQ
The reason for requesting this is there is occasionally a single sample that may have had a bad call at a site. Using the "KEEP_IF_ALL_UNFILTERED" filters N-1 high quality calls. However, on the other extreme, if we use "KEEP_IF_ANY_UNFILTERED" and only a single sample passes the filters, we introduce N-1 low quality calls and assert that they pass our requisite filters. The requested hybrid method will keep all information from the input samples and allow for better granularity.
John Wallace
I've noticed a small bug with GATK tools and VCF files. CombineVariants and GenotypeGVCF can generate files where some samples have fewer fields than the format column.
For instance, this is part of a line from the VQSR-ed output VCF of GenotypeGVCF: 1 15820 rs200482301 G T 5909.59 VQSRTrancheSNP99.90to100.00 AC=21;AF=0.154;AN=136..... GT:AD:DP:GQ:PL 0/0:.:40:66:0,66,990 0/0:.:41:69:0,69,1035 1/1:0,20,1:21:78:985,78,0 0/0:.:35:60:0,60,900 ./.:.:1 0/0:.:7:21:0,21,233 ..............
The second to last sample entry is ./.:.:1 (3 fields), while the format entry is GT:AD:DP:GQ:PL (5 fields). I think that GT=./., AD=., and DP=1, so the data is not getting messed up. This might even be within the rules of VCF, but one of the software that I use will not parse VCF files when 1 < # sample fields < # format fields. If sample entries were extended by ":." for every empty FORMAT field (unless only . or ./. was present in sample column), it would make the file parsable.
It's not too hard of a manual fix, but it might be nice to add the functionality into the toolkit. I've seen it happen with CombineVariants as well, when the input VCF files have different numbers of FORMAT fields.
When using HaplotypeCaller's '--emitRefConfidence', with both GVCF and BP_RESOLUTION, we get lines like this one:
1 2337032 rs1129171 C T,<NON_REF> 480.77 . BaseQRankSum=0.218;ClippingRankSum=0.103;DB;DP=45;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQ0=0;MQRankSum=-1.344;ReadPosRankSum=1.046 GT:AD:DP:GQ:PL:SB 0/1:19,26,0:45:99:509,0,330,565,407,97
The new 3.0 tool GenotypeGVCFs has no problem processing these lines. However CombineVariants fails to run with this message:
##### ERROR MESSAGE: Reference records should not have more than one alternate allele
By looking at the relevant code:
if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) {
if( vc.getAlternateAlleles().size() > 1 ) { throw new IllegalStateException("Reference records should not have more than one alternate allele"); }
Sounds like the presence of
<NON_REF> in lines with ALTs is triggering this exception.
I also looked at this forum entry and the example there doesn't have
<NON_REF> in lines with ALTs.
"Using the reference confidence calculation mode & generating a GVCF"
Should I be able to run CombineVariants on files produced using '--emitRefConfidence'?
Thanks, Carlos PS: I tried to include links to github and GATK forum, but the spam filter seems not to like that.
Is there a way to pass a file containing a list of vcfs to CombineVariants --variant? I tried naming it with .list, but I get a tribble error.
I believe that I may have found an issue with the CombineVariants tool of GATK that manifests itself when there is a repeated ID in a given VCF. For us, the reason to have repeated IDs in a VCF file is to detect inconsistencies in our sample by calling variants on 2 different DNA samples and then checking the concordance. Our current process is:
1) Generate a VCF containing unique IDs (using GATK CallVariants)
2) Replace the VCF header with potentially non-unique IDs (using tabix -r)
3) Merge a single VCF to uniqify the IDs (using GATK CombineVariants)
It seems that the genotypes in the merged VCF are off by one column. I've attached 3 files that demonstrate the issue: "combined" which is the result of step 1, "combined.renamed", which is the output of step 2, and "combined.renamed.merged", which is the output of step 3.
The relevant lines are as follows:
Using the depth argument here, we can see that in the merged dataset, NA12801 has depths 290,293 whereas in the original and renamed datasets the depths were 127,127. The 290,293 depths correspond to HG00423, which is the column before.
I have confirmed this behavior in both GATK 2.7-4 and 2.8-1. If there's any more information that you need, please let me know, and I would be happy to provide it. Also, if you might know where this issue arises, I would be happy to try to provide a patch.
John Wallace
Hi team,
I've been having some issues with DP following CombineVariants:
I have two vcf files called by different callers - one by GATK UnifiedGenotyper and the other by samtools mpileup.
When I merge the files using CombineVariants, I notice that the DP per each variant is actually equal to the sum of DP of each of the vcf files. For example: If for a shared variant in both vcf files the DP=8, then the DP in the union file will be DP=16. Neverhteless, if a given variant is not shared by both files, then the DP in the union file will be equal to the input file.
Is there a way resolve this issue?
Hi sir, I used GATK combine variants to call SNP from my 7 vcf files. Now I am using unified genotyper to call all samples simultaneously for SNP. When I focused on my gene of interest (DLX6), in combine variants output, there are 5 "./." among 7 samples. but in case of multisample SNP calling, DLX6 gave 0/0 in those samples and its corresponding information. So, I want to know what is the meaning of "./." in combine variants results and which results should I take for analysis?
I am using CombineVariants to combine two multisample vcfs from made from HaplotypeCaller. The vcfs cover the same genomic region, and do not overlap in sample names. I have noticed some potential issues reporting AD and PL fields after running CombineVariants.
If the site was multiallelic in one vcf but biallelic in the other vcf, then the AD and PL fields are omitted altogether, such that GT:DP:GQ is what is reported in the combined file - I am guessing this is expected behavior?
however, if the site was biallelic in both vcfs, or monomorphic on one vcf but polymorphic in the other, the AD and PL fields are reported, but the numbers do not make sense.
my command line:
GATK -T CombineVariants -R ~/Capsella_rubella_v1.0_combined.fasta -V sc1_HC_94samp.vcf -V sc1_HC_set2.vcf -nt 20 -o sc1_HC.vcf &
original vcf record:
scaffold_1 3275 . G T 1170.18 . AC=2;AF=0.011;AN=188;BaseQRankSum=0.295;ClippingRankSum=-1.233;DP=5815;FS=1.186;InbreedingCoeff=-0.0106;MLEAC=1;MLEAF=5.319e-03;MQ=98.00;MQ0=0;MQRankSum=3.414;QD=9.36;ReadPosRankSum=1.761
combined vcf record:
scaffold_1 3275 . G T 1170.18 . AC=3;AF=7.979e-03;AN=376;DP=11787;MLEAC=1;MLEAF=5.319e-03;MQ0=0;set=Intersection
is this a bug? or am I missing something about how to use CombineVariants? thanks much for your help!
I'm analyzing seven trio exomes right now with the latest GATK (version 2.7-4-g6f46d11), and was surprised to find a large number of mendelian violations reported by PhaseByTransmission, even after eliminating low/no coverage events. Tracking down the problem, it seems that CombineVariants occasionally propagates the PL field to the new vcf file incorrectly, sometimes in a way which causes GT not to correspond to the lowest PL.
Here's an example, showing just the GT, AD, and PL columns for a few positions in one trio. For each position, the first line contains the genotypes from the original vcf file, and the second shows the genotypes from the merged file.
#CHROM POS ID REF ALT 100403001-1 100403001-1A 100403001-1B 1 5933530 rs905469 A G 0/0:37,0:0,99,1192 0/0:35,0:0,90,1101 0/0:44,0:0,117,1412 1 5933530 rs905469 A G 0/0:37,0:189,15,1192 0/0:35,0:0,90,1101 0/0:44,0:0,117,1412 1 10412636 rs4846215 A T 0/0:119,0:0,358,4297 0/0:113,0:0,337,4060 0/0:102,0:0,304,3622 1 10412636 rs4846215 A T 0/0:119,0:110,9,0 0/0:113,0:0,337,4060 0/0:102,0:0,304,3622 1 11729035 rs79974326 G C 0/0:50,0:0,141,1709 0/0:53,0:0,150,1788 0/0:71,0:0,187,2246 1 11729035 rs79974326 G C 0/0:50,0:1930,0,3851 0/0:53,0:0,150,1788 0/0:71,0:0,187,2246 1 16735764 rs182873855 G A 0/0:54,0:0,138,1691 0/0:57,0:0,153,1841 0/0:47,0:0,120,1441 1 16735764 rs182873855 G A 0/0:54,0:174,0,1691 0/0:57,0:0,153,1841 0/0:47,0:0,120,1441 1 17316577 rs77880760 G T 0/0:42,0:0,123,1470 0/0:38,0:0,111,1317 0/0:53,0:0,153,1817 1 17316577 rs77880760 G T 0/0:42,0:233,17,1470 0/0:38,0:0,111,1317 0/0:225,25:0,153,181 1 28116000 rs2294229 A G 0/0:37,0:0,105,1291 0/0:37,0:0,111,1379 0/0:30,0:0,87,1066 1 28116000 rs2294229 A G 0/0:37,0:0,105,1291 0/0:37,0:0,111,1379 0/0:30,0:1844,159,0 1 31740706 rs3753373 A G 0/0:123,0:0,349,4173 0/0:110,0:0,319,3793 0/0:111,0:0,328,3885 1 31740706 rs3753373 A G 0/0:123,0:117,6,0 0/0:110,0:0,319,3793 0/0:111,0:0,328,3885
Most genotypes are propagated correctly, and in fact, which a propagated incorrectly changes from run to run.
In my case, I'm merging files from disjoint regions, so I can work around the problem, but it would be nice if this were fixed.
Thanks, Kevin
Hi! This is my code:
java -Xmx4g -jar GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar \
-R genome.fa \
--filter_reads_with_N_cigar \
-T CombineVariants \
-V:NORMALSpost RNA-edit_SNPs_NORMALS-post_SNPeff_VA.vfc \
-V:OMNI 1000G_omni2.5.hg19.vcf \
-V:db137 dbsnp_137.hg19.vcf \
-V:Hapmap hapmap_3.3.hg19.vcf \
-V:ESP1,VCF ESP6500SI-V2-SSA137.updatedRsIds.Allchr.snps_indels_FIX.vcf \
--out NORMALS-post_TruePositives_raw.vcf &&
java -Xmx4g -jar GenomeAnalysisTK.jar \
-R genome.fa \
--filter_reads_with_N_cigar \
-T SelectVariants \
-V NORMALS-post_TruePositives_raw.vcf \
-select "set == 'NORMALSpost'" \
--out NORMALS-post_TruePositives.vcf
I hope I got this right: I now have SNPs (I have only called SNPs, not indels) that is found in my sample, 1000G, dbSNP and ESP. Right?
Question: Can I easily make a VCF with all SNPs in MY sample only, not found in anything else by tweaking this code? Or must I do it some way else?
Hi! Sorry for my ignorance, but the ESP files contains 24 vcd in total. I tried to include them all on CombineVariants, but gets an error. I have tried to merge the 24 file to one, both with vcftools and picard, failing with both..
Somebody knows?
Thank you!
If I want to merge different VCF files, which I used -L argument for calling variants against to different chromosomes individually with the same list of samples by HaplotypeCaller. I mean the sample are the same, I just used -L to call variants chromosome by chromosome separately. I suppose whether catVariants or CombineVariant will give me the same results, right ?
Hi! The title says it all. Im trying to narrow down my vcf. Which tools is good to answer this question?
I have tried this:
java -Xmx4g -jar GenomeAnalysisTK.jar \ -R genome.fa \ --filter_reads_with_N_cigar \ -T CombineVariants \ -V:COHORT1 path \ -V:COHORT2 path \ --filteredAreUncalled \ -o path
But the output seams incomprehensibly massive!
is there any way to combine a snp vcf and indel vcf (generated with the UnifiedGenotyper) later? in the way that there is only one row per locus?
regardless how I combine (I tried mainly CombineVariants), if there is something different called in the two vcf files in one locus, there are two rows in the combined one; I would like this called/written as alternatives for one locus
I'm working with different tools to call variants (GATK is one of them) for the same sample and I'm merging these results with
gatk -T CombineVariants -R ucsc.hg19.fasta -V:GATK GATK.vcf -V:OTHER OTHER.vcf -o combined.vcf -genotypeMergeOptions PRIORITIZE --rod_priority_list GATK,OTHER
But when I have a discrepancy between results (I mean, same chr and pos, but different call), I just get GATK's result in my result file, Is there any way to have both calls when I have discrepancies? I don't want to use -genotypeMergeOptions UNIQUIFY.
chr17 7917905 . C T 360.16 . [...] GT 0/1
chr17 7918012 . C T 896.16 . [...] GT 0/1
chr17 7917905 . C T 360.16 . [...] GT 0/1
chr17 7918012 . C T 896.16 . [...] GT 1/1
chr17 7917905 . C T 360.16 . [...];set=Intersection GT 0/1
chr17 7918012 . C T 896.16 . [...];set=Intersection GT 0/1
What I want to obtain:
chr17 7917905 . C T 360.16 . [...];set=Intersection GT 0/1
chr17 7918012 . C T 896.16 . [...];set=GATK GT 0/1
chr17 7918012 . C T 896.16 . [...];set=OTHER GT 1/1
Hi, I'm calling Variants with HaplotypeCaller in a population of 2 Parents and 7 F1-individuals. After read backed phasing I'm combining the vcf files of my genotypes with CombineVariants. In the outfile I very often find "./.". I thought this means there is no coverage at a certain position. But at many positions I do have good coverage. Why do I then get ./.? Moreover I used FastaAlternateReferenceMaker and created a new reference sequence including the variants from the parents. In that case, after I run HC and do the phasing and combine variants steps, I only get "./." at positions where there is really no coverage (as I can see in my mappings). Nadia
my two VCF files have different alternate allele at the same position as i have called the variants using two different callers. When i run combine Variants on the both my GT field is not updated properly. AD field is also not updated properly but i ran Variant Annotator and that fixes that issue.
chr1 87708015 rs58006838 C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.479;DB;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;QD=10.41;ReadPosRankSum=0.925 GT:AD:DP:GQ:PL 0/1:3,9:14:37:174,0,37
chr1 87708015 . C A . PASS AN=2;DP=4;NS=1 GT:AD:DP:GQ 0/1:2,2:4:8.42
Merged VCF file:
chr1 87708015 rs58006838 C T,A 145.77 PASS AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.479;DB;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;NS=1;QD=10.41;ReadPosRankSum=0.925;set=Intersection GT:AD:DP:GQ **0/1**:3,9,2:14:37
command used:
java -jar $gatk/2.7-1-g42d771f/GenomeAnalysisTK.jar -T CombineVariants -V one.vcf.gz -V two.vcf.gz -o test.vcf -R $ref
Is this a known limitation or a bug?
So today I have to compare two different vcf (from different pipelines, only one of them is from GATK) and when I tried to combine it with combineVariants, I had an error because the references doesn't match:
The provided variant file(s) have inconsistent references for the same position(s) at chr1:1724719, A* vs. G*
I know why it's happening, but I don't know if there is an option/tools to "fix" the vcf from the other pipeline.
That I want to do is take the VCF created with a "bad" reference and use a command or GATK option to "fix" it according with the correct reference fasta file.
Thanks for your help!
I've seen related issues discussed here but not exactly this one. I'm following closely the current recommendations for an exome pipeline, and the GATK version,downloaded from git, was v2.5-2-gf57256b, Compiled 2013/06/06 17:28:57.
For example, I have two samples with heterozygous variants 12:81503433C>G. The AD values for the the samples in the raw vcf file, and the SNVs-only file were 15,14 and 20,15 for the two samples and these agree with what I see in IGV. There was nothing in the indels-only file at that position. The AD values were the same in the recalibrated SNVs-only file. But after combining the recalibrated SNVs and indels with CombineVariants the AD values inexplicably became 21,0 and 0,24 respectively. This seems to be happening to many variants.
-T CombineVariants -genotypeMergeOptions UNIQUIFY Is UNIQUIFY the default? I want every variant in the output file with each individual in the same column
When using CombineVariants, my variants get a FILTER value of either PASS or LowQual. Would it be possible to add an option to CombineVariants which prevents the FILTER value to be set to PASS? Otherwise I have to do some file processing before I run ApplyRecalibration further downstream. It would be great if this was a feature of all walkers and not just VariantFiltration. I'm not sure if the forum is the right place for feature requests. Happy to use Bugzilla or similar instead. Thanks.
I have a set of VCFs with identical positions in them:
If I use all of them as input for VariantRecalibrator, which annotations will VariantRecalibrator use? Should I instead merge the VCFs with CombineVariants and run VariantAnnotator, before I run VariantRecalibrator?
I'm not sure if the forum is for asking technical questions only or you are allowed to ask for best practices as well. Feel free to delete my question, if it doesn't belong here. Thank you.
I called variants in chunks (100000 bp chunks) on chromosome 20 on 450 reduced BAMS using -T UnifiedGenotyper, which resulted in the generation of 631 VCFs.
Now I want to combine these 631 VCFs using -T CombineVariants, however there seems to be a problem with some of the VCFs and all I get is an error message.
I can combine the 5 first VCFs that were generated, but when I add a sixth one (chr20:400000_500000) I get the following error:
##### ERROR MESSAGE: For input string: "20"
If I exclude that file, I can combine about 30 VCFs until I encounter a similar error message for a different VCF file:
##### ERROR MESSAGE: For input string: "120"
I've looked through both of the "problematic" VCFs and can't see how they differ from the ones that I can combine.
Any idea of what may be going wrong and how I can solve this? At the moment I can only identify problematic VCF by trying to combine them using CombineVariants since I don't know what it is about these particular VCF files that is causing the problem.
Thanks for your help, Tota
Hi. I want to merge two VCF files. Initially I was selected only indels(by select variant option). Now I want to merge these two VCF file which contains only INDELS. But When I run the command, I am getting the same error:
##### ERROR stack trace
java.lang.NumberFormatException: For input string: "."
I run this command:
java -jar -Xmx2g GenomeAnalysisTK.jar -R hg19_5.fasta -T CombineVariants -V indelsample1.vcf -V indelsample3.vcf -o indels1s3.vcf -genotypeMergeOptions UNIQUIFY
Could you please tell me what is the reason behind this? and how to merge two VCF file having INDELS?
Thanks in advance.
I am trying to merge two vcfs (SNVs and INDELs) from the same sample. The problem appears to be that the INDEL vcf defines "combined_sample_name" but the SNV vcf does not. So when I merge I get two sample columns. How can I force GATK to treat them as a single sample?
I tried --assumeIdenticalSamples to do a "simple merge," but that made no difference.
As a side note, these vcfs are from an Ion Torrent machine.
java -jar $GATK \
-T CombineVariants \
--assumeIdenticalSamples \
-V:${baseFolderName} ${i}/SNP_variants.vcf \
-V:${baseFolderName} ${i}/indel_variants.vcf \
-o ${RESULTS_DIR}/${baseFolderName}_variants.vcf
I'm just reverse engineering a colleagues script and I've noticed they're using CombineVariants in PRIORITIZE mode but without a -priority argument. I've looked at the documentation and I can't see what the defined behaviour would be in this situation. Would default priority in this situation follow the order of the arguments supplied; the reverse order; or random?
Thanks, Martin
Nevermind, from what I can see from the source it should be erroring out if -priority is not supplied. I must have missed something in the pipeline script.
Edit 2: No wait
if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null )
throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes");
is pointless because this is run first in initialize:
if ( PRIORITY_STRING == null ) {
PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
This should follow the input order yes? Unless vcfRods.keySet is sorted?
I used Beagle to phase my data but for some indels, I have some probleme :
example :
Input vcf :
Input for beagle created by ProduceBeagleInput:
Output vcf created by BeagleOutputToVCF:
error message by CombineVariants:
MESSAGE: Badly formed variant context at location 68599872 in contig 2. Reference length must be at most one base shorter than location size
Can you help me?
Dear team, I am new to GATK and I am having a hard time simply trying to merge vcf files. I have tried to solve the problem by referring to the guide and to previous posts, but nothing woked. Actually I found several discussions about the very same error message I receive, but it seems that no clear answere was provided. Here is this message:
I have tried three different MS Dos commands to do the task (see belbow), but the message didn't change:
1. java -jar GenomeAnalysisTK.jar -T CombineVariants -R E:\RessourcesGATK\ucsc.hg19.fasta -V:sample1 E:\TestGATK\sample1.vcf -V:sample2 E:\TestGATK\sample2.vcf -o combined.vcf
2. java -jar GenomeAnalysisTK.jar -R E:\RessourcesGATK\ucsc.hg19.fasta -T CombineVariants --variant E:\TestGATK\sample1.vcf --variant E:\TestGATK\sample2.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY
3.java -jar GenomeAnalysisTK.jar -R E:\RessourcesGATK\ucsc.hg19.fasta -T CombineVariants --variant E:\TestGATK\sample1.vcf --variant E:\TestGATK\sample2.vcf -o output.vcf -genotypeMergeOptions PRIORITIZE -priority foo,bar
I have also tried to use the reference human_g1k_v37.fasta as a resource, but it was the same. I have suppressed the # before CHROM in the header line, tested vcf generated by Samtools or by GATK, but it did not change anything. Is this a problem of environment? I haven't read anything mentioning that GATK could not work with MS Dos.
Thank you very much for your help. S.
When I run CombineVariants on two vcf files with variants at the same position but with different REF alleles and also different sets of ALT alleles, the AD fields for the genotypes are not updated to reflect the changes in the ALT field. The REF and ALT fields and the GT field for each genotype are all correctly updated. For example combining
3 10128965 rs71052293 CTT CT,C,CTTT 19936.43 PASS AC=1,1,1;AF=0.25,0.25,0.25;AN=4 GT:AD:DP:GQ:PL 0/2:115,0,33,12:230:6.96:980,1237,2795,0,946,1900,7,679,467,817 3/1:97,13,20,16:229:99:804,221,832,581,176,3047,521,0,1653,1595
3 10128965 rs71052293 CT C,CTT,CTTT 14280.61 PASS AC=1,1,1;AF=0.25,0.25,0.25;AN=4 GT:AD:DP:GQ:PL 2/1:110,20,33,18:237:1.90:850,289,1027,457,0,1487,147,877,2,1858 0/3:80,48,5,29:209:99:1835,875,977,2101,1119,3322,0,142,331,462
3 10128965 rs71052293 CTT CT,C,CTTT,CTTTT 19936.43 PASS AC=2,1,2,1;AF=0.250,0.125,0.250,0.125;AN=8;set=Intersection GT:AD:DP:GQ 0/2:115,0,33,12:230:7 3/1:97,13,20,16:229:99 3/1:110,20,33,18:237:2 0/4:80,48,5,29:209:99
There five alleles (one REF and four ALT) but only four AD fields for each genotype.
My command line:
java -jar -Xmx4g GenomeAnalysisTK.jar -T CombineVariants -R human_g1k_v37.fasta -V test_input1.vcf -V test_input2.vcf -o test_combined.vcf
Is this a known limitation or a bug?


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Epson V11H395020
V11H395020 3500 lumens PowerLite D6150 Multimedia Projector
Boasting a robust design, advanced networking capabilities and cost-efficient maintenance features, the PowerLite D6150 is the perfect solution for lecture halls and corporate conference rooms alike. Featuring a dust- ...
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Dukane 8103H
8103H Ultra Short Throw LCD Projector
The 8103H is 3000 lumens and has an ultra short throw lens. Perfect for interactive whiteboards, screens and any projection situation where you want an easy install with minimal wiring needs.
Write a Review
Epson V11H396020
V11H396020 3500 Lumens PowerLite D6155W Multimedia Projector
Boasting a robust design, advanced networking capabilities and cost-efficient maintenance features, the PowerLite D6155W is the perfect solution for lecture halls and corporate conference rooms alike. Featuring a dust ...
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Sanyo PLCXU111
PLC-XU111 XGA (1024 x 768) LCD Multimedia Projector, 4000 ANSI Lumens, 7.7 lbs
The Sanyo PLC-XU111 XGA LCD Multimedia Projector is perfect for both education and business presentations. The outstanding brightness level of 4,000 ANSI Lumens, allows bright and crisp presentations even in a well-lit c ...
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Sanyo PLV80L
PLV-80L 16:9 Widescreen WXGA (1366 x 768) Home Theater Multimedia Projector Without Lens, 3000 ANSI Lumens, 17.4 lbs
The LCD panel achieves high-resolution (1366 x 768) with a high contrast ratio. This provides outstanding picture quality that makes your presentations rich and lifelike. Additional features include digital progressive s ...
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DLA-RS40U Reference Series 3D-Ready Home Cinema Projector
Never has so much performance been packed into a home theater projector as economical as JVC's DLA-RS40U. Whether its movies in 2D, 3D, live sporting events, or concerts, the DLA-RS40 will please the most discerni ...
(1 Reviews)
Panasonic PTAE1000U
PT-AE1000 1100 ANSI Lumens Wide-Screen LCD Home Theater Projector
The Panasonic PT-AE1000U is a native high-definition home theater projector that produces stunning, film-like images with a dramatic 11000:1 contrast ratio. The projector is equipped with advanced digital picture-enhanci ...
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Dukane 8944
8944 XGA 4000 Lumen Projector
The ImagePro 8944 is a LCD projector that can be used in a variety of applications. With sufficient brightness for most classrooms and conference rooms the 8944 is designed to be reliable and easy to maintain.
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BenQ W6000
W6000 Corporate/Home Entertainment Projector with 2500 Lumens, 50,000:1 Contrast Ratio, Full HD Native Resolution (1920 x 1080), 720p, 1080i, 1080p/60/50/24 HDTV and NTSC, PAL, SECAM
The full HD resolution BenQ W6000 Corporate/Home Entertainment Projector creates a unique theater experience wherever it's used. Its 2500 ANSI lumens of projection power combined with a 50,000:1 contrast ratio is your as ...
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Hitachi CPX615W
CPX615W CP X615 - LCD projector
CP-X615W Hitachi CP X615 - LCD projector
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Eiki LC-XGC500L
LC-XGC500L 3LCD Projector With 5000 ANSI Lumens & XGA 1024 x 768
The LC-XGC500L makes maintenance easier and time between cleaning longer thanks to the top-accessed lamp and filter and cartridge air filter system which automatically advances to a fresh filter.
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Panasonic PTF100U
PT-F100U 3200 Lumens Permanent-Installation LCD Projector
The Panasonic PT-F100U projector features Lens Shift and a 2x zoom, placed on a shelf. All of this makes this high-performance projector perfect for the meeting or class room.
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Sanyo PLCWXU30
PLC-WXU30 WXGA 3700 ANSI Lumens LCD Multimedia Projector
The Sanyo PLC-WXU30 projector makes it possible to project high-quality HD images from virtually any location. At 3700 lumens, this extremely bright, yet compact, projector is equally comfortable entertaining the whole f ...
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Sharp PGD50X3D
PG-D50X3D DLP Projector 5000 ANSI Lumens XGA (1024 x 768)
The 3D Ready Sharp PG-D50X3D BrilliantColor DLP Projector incorporates DLP Link technology for high quality 3D projection from a single projector. In addition to operating as a traditional �2D� projector, this future-pro ...
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Sanyo PLCXU305
PLC-XU305 LCD Projector with 3000 ANSI Lumens
Sanyo is the first in the industry to provide a simple wireless projection setting with the PLC-XU305. What could be simpler? Just plug in the SANYO USB memory terminal provided, and you're a click away from automaticall ...
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Canon 2223B002
REALIS SX7 4000 Lumens SXGA+ Projector
Around the world, Canon products are synonymous with optical excellence, advanced image processing, and superb performance. Canon projectors are no exception. The family of Canon projectors includes the REALiS line of br ...
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Eiki LC-XL200L
LC-XL200L LCD Projector With 6000 ANSI Lumens & XGA 1024x768
Combining large venue projection features with durable components and reduced maintenance, here�s a projector that delivers big screen performance on a budget. The EIKI LC-XL200 comes complete with a wide-range power zoo ...
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Dukane 8918
8918 LCD XGA 3500 Lumens Projector
The ImagePro 8918 is a LCD projector that can be used in a variety of applications. With sufficient brightness for most classrooms and conference rooms the 8918 is designed to be reliable and easy to maintain. ...
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InFocus C350
C350 ASK Proxima XGA (1024 x 768) DLP Multimedia Projector, 3500 ANSI Lumens, 7 lbs (3.2 kg)
Featuring 3500 max ANSI lumens with 2000:1 contrast ratio and an XGA-resolution DLP chipset, the C350 is a powerhouse. Whether its a bright conference room without any light control or a massive meeting space requir ...
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MP780ST Short Throw 3D Ready DLP Projector With WXGA 1280x800 Resolution & 2500 Lumens Point Draw
The MP780 ST DLP Projector from BenQ is an attractively priced projector that's as useful in the living room as it is in the conference or the classroom. At 2500 ANSI lumens backed with a crisp 3000:1 contrast rat ...
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Sharp PGD40W3D
PG-D40W3D DLP Projector 4000 ANSI Lumens WXGA (1280 x 800)
The 3D Ready Sharp PG-D40W3D Projector offers 4000 ANSI Lumens, WXGA (1280 x 800) native resolution and BrilliantColor� DLP� technology at a very affordable price. Incorporating DLP� Link� technology, the PG-D40W3D enabl ...
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Eiki EIP-5000L
EIP-5000L DLP Projector With 5200 ANSI Lumens & XGA 1024 x 768: Lens Not Included
The EIP-5000L is a conference/boardroom projector that offers 5000 ANSI lumens of brightness, 1200:1 contrast ratio, XGA resolution output and an 8-power digital zoom. It utilizes the DLP� imaging technology which delive ...
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Panasonic PTD7500U
PT-D7500U XGA 5000 Lumen
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Optoma TH1060
TH1060 3500 ANSI Lumens 1920 x 1080 DLP projector - HD 1080p
The Optoma TH1060 HD 1080p DLP Projector is an ideal choice to meet both the rigors of business use and the demands of discerning home theater enthusiasts. Quality starts with the 1080p resolution, a perfect mate for ...


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Pronunciation: (skā'bēz, -bē-ēz"), Strict Standards: Non-static method FenSites::linkTo() should not be called statically in /site/html/dictionary/scabies.html on line 73 [key]
—n. (used with a sing. v.) Pathol., Vet. Pathol.
a contagious skin disease occurring esp. in sheep and cattle and also in humans, caused by the itch mite, Sarcoptes scabiei, which burrows under the skin. Cf. itch (def. 10), mange.
Random House Unabridged Dictionary, Copyright © 1997, by Random House, Inc., on Infoplease.
See also:


text:
Welcome to SIAM at Tufts!
The Tufts chapter of the Society for Industrial and Applied Mathematics promotes exploration in applied mathematics for the student communities at Tufts.
Meetings are held every other Wednesday from 12:00pm to 1:15pm in either the Clarkson Conference Room or Classroom 101 in Bromfield-Pearson, unless otherwise noted.
Upcoming Events
March 4, 2015
Speakers: Kye Taylor, PhD, Mathematics Department, Tufts University
Title: Reordering of image pixels using patches to achieve image compression
Abstract: Recent improvements in computing demand the processing and analysis of very large datasets in the form of matrices in a variety of fields. Often the analysis requires the creation of low-rank approximations to the matrices for the purpose of compression. In this talk, I will present a new approach to compressing images. This approach identifies an image as a series of non-overlapping contiguous patches, and compresses a reordered version of the image matrix based on these patches. Low-rank approximations can then be utilized once a reordering of the pixel entries of the matrix is performed. I will demonstrate the approach when using the Singular Value Decomposition (SVD) and Nonnegative Matrix Factorization (NMF) low-rank approximations. I will also demonstrate that the approach produces better quality image reconstructions using less memory for a smaller computational cost than when compressing without reordering.


text:
Written on: 08/08/2010
We bought a Samsung RSH1DGRS, and after a couple of years we had a fault on it in the fridge part. We phoned around for some quotes to repair it, and in the end we ordered a kit online from Appliance DIY Repairs and did it ourselves. It took about an hour, but it was worth it for the money we saved and just to get it cold again. If we get any problems in the future, we'll just go back to Appliance DIY Repairs, and ask them what we should do.
As rated by real users
" Very disappointed with this quality Miele fridge freezer. " Read More
Written by Cadge1966
" Brilliant " Read More
" Excellent service from Applicance Direct " Read More
Written by clarevincent
" Ff187e " Read More
" Liebherr fails after 3yrs " Read More


text:
Slain Toddler's Mom Pleads Guilty To Charges
The mother of a 1-year-old Maryland boy found dead in central Ohio has pleaded guilty to involuntary manslaughter and tampering with evidence.
Listen to the Story
Families who need help the most this holiday season picked up presents donated to them through the Salvation Army's Adopt-A-Family program yesterday.
A Salvation Army volunteer rolls a large, plastic cart carrying gifts toward a family waiting to load their car. Some of the presents are already wrapped in colorful Christmas paper.
Susan Sayer's trunk is filled with diapers and baby toys. Sayer lives in Columbus with her boyfriend and five month old son. She said Christmas would not have been possible this year without the help from others.
"I was homeless for a little bit. I spent probably three weeks in the shelter. I got on my feet real quick and got a job and everything like that; got my apartment. And now everything is going the way it is supposed to be," Sayer said.
Local individuals, churches, businesses and schools "adopt†families, like Sayer's, and fulfill their wish lists. Five-hundred-eighty families received help this year. The Salvation Army's Kelli Trinoskey said that's a 16 percent increase compared to last year.
"Maybe just really fell hard on their feet and they need a little leg up. We've already helped many of them secure housing or jobs or food through our food pantry. There was just no way could they provide Christmas this year," she said.
Shawntae Townsel lives on the city's West Side. Townsel said she and her three small children were at a shelter for part of the year. The program, she said, will help put a few gifts under the tree.
"Baby dolls and coloring books – what my kids like – and cars for my sons. That's it. It wasn't really nothing major," Townsel said.
Another mother is grateful to Salvation Army volunteers who maneuver a second bike into her car's back seat.
"It's just a little stuck," a volunteer said.
"Thank you so much! God bless," the woman said.


text:
commercial property for rent or lease in Rector (PA), Industrial Space For Lease.
Rector commercial real estate for lease, rent,, and leased investments.
Find Rector industrial buildings for lease, retail rentals, & Rector shops. Locate a Rector warehouse lease and any real estate for lease / investment, including industrial properties to rent and sale.
Some Rector commercial businesses may be more productive and efficient if they have adequate office area. In some areas the monthly lease on such areas can very often make up a substantial amount of a small company's budget. Sometimes its feasible to share facilities like conference rooms with other tenants, to reduce costs. Consider different options before taking out a long-term lease on a large workplace when the possibility may exist that your business could outgrow the areas quickly. Consider short-term rentals for companies that are growing and in transition.
commercial space listings
Rillton (Westmoreland), Latrobe, Northern Cambria (Cambria), Scottdale, Heilwood (Indiana), Vandergrift, Alverda, Schenley (Armstrong)
in Rector Pennsylvania (PA) (Westmoreland)


text:
About Us -
Your Best Resource for Sports Travel
Founded in 2000, Sports Traveler has continued to expand to provide our clients with the largest, most comprehensive selection of sports travel available.
Our large network of sporting event travel options include sports travel packages, event tickets, and hotel rooms for all major sporting events worldwide.
Mission Statement:
To treat every client as an individual
and to provide that individual
with the finest travel options available to suit their needs
There is something here for every Sports Travel Enthusiast.
Our extensive directory of sports travel options to every major sporting event in the world offers individual travelers, corporate groups, and VIP clientele the largest selection of sports travel available. At Sports Traveler there is an option available for every budget and interest. Let us be your one and only stop for sports travel.
Purchase with confidence.
Every tour operator within our network has been pre-screened and qualified to be a Sports Traveler partner. We take pride in offering our clients only the finest sports travel available so you can rest assured that your sports travel experience will exceed your expectations.
Our Customers are #1.
We take every client's travel plan's seriously. No purchase is too small. We are continually at your service and available to answer questions or concerns from the time of purchase throughout the event.
Additional Information:
|2015 NCAA Final Four Tournament
|Apr 04
|Indianapolis, IN
|Masters Golf Tournament
|Apr 06
|Augusta, GA
|Kentucky Derby
|May 02
|Louisville, KY
|Talladega Aaron's 499
|May 03
|Talladega, AL
|Kansas STP 400
|May 09
|Kansas City, KS
|Preakness Stakes
|May 16
|Baltimore, Maryland
|Charlotte Coca Cola 600
|May 24
|Concord, NC
|Dover Downs FedEx 400
|May 31
|Dover, DE
|Indianapolis 500
|May 31
|Indianapolis, IN
|Belmont Stakes
|Jun 06
|Elmont, New York
|Party at the Pocono's 400
|Jun 07
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|Michigan Quicken Loans 400
|Jun 14
|Brooklyn, MI
|U.S. Open Golf Tournament
|Jun 18
|University Place, WA
|Daytona Coke Zero 400
|Jul 05
|Daytona Beach, FL
|MLB All Star Game Week
|Jul 13
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|U.S. Open Tennis Championships
|Aug 31
|Flushing, New York
|Breeders Cup
|Oct 30
|Lexington, KY
|Texas AAA 500 Race
|Nov 08
|Fort Worth,TX
|Rose Bowl
|Jan 01
|Pasadena, CA
|Sugar Bowl
|Jan 01
|New Orleans, LA


text: |Faith Like Potatoes is an inspiring true story of a rugged South African farmer, Angus Buchan, and is set in the turbulent hills of the KZN Midlands. Angus' manic quest for material success is slowly transformed into a wild love for God and people, as he wrestles with faith, hope, natural disasters and tragic personal loss. Item No: 17514 Vendor: Provident Distribution


text: Kumho Ecsta STX (KL12) 3.9 (56 reviews) Price Range: USD $126.99 to $1,339.99 All Season PRODUCT IS CURRENTLY NOT AVAILABLE FOR PURCHASE Light Truck and SUVs / All Season / High Performance The ECSTA STX meets the demanding needs of the SUV/ light truck UHP and tuner market. Engineered to provide "extreme performance and eye appealing appearance" for a full size range of sizes from 15" through 26". The all season performance provides all-out wet and dry handling that has been previously reserved for passenger tires. Unprecedented tire performance. For the safety of your family. For comfort when you are driving. For an expression of your pride, the ECSTA SPT KU31 has been developed by Formula Technology Special high performance tread compaound maximizes traction in both wet and dry.High strength steel belts, covered with a spiral wrapped nylon cap ply, provides excellent durability and handling.High bead apex design optimizes the tire for good ride comfort with excellent steering response. Share this tire: HAVE A QUESTION? 1-877-877-1010 ASK AN EXPERT! LIVE CHAT FITMENT GUARANTEE All orders are verified for fitment guarantee. Helpful Resources Shipping Information Frequently Asked Questions Customer Reviews Sizes & Prices Sort By: Sort by Dry Wet Snow Handling Comfort Noise Treadwear Overall 3.9 Kumho Ecsta STX (KL12) Rate Now Dry (4.5) Wet (4.1) Snow (1.9) Handling (4.2) Comfort (3.7) Noise (3.2) Treadwear (3.3) Overall: 4.8 Dry 5.0 Wet 5.0 Snow 4.0 Handling 5.0 Comfort 4.0 Noise 4.0 Treadwear 5.0 Original Goodyears got 19500 miles before balded... poor handling. Kumho STX's got 72000 miles, wore flat and the handling was way beyond expectations. Replaced the Kumho's with Hankook Ventus tires and am sorely disapointed not only with the handling, but also with the tire's treads scalloping on the inner and outer edges (shoulder Ribs). Am definitly going back to the Kumho's next tire replacement. I have recommended the STX's to many friends... all are very pleased! Size: Vehicle: 115848 KM of Tire Wear Anonymous made this review on 1/1/2011 and is a Aggressive Driver (Hard Cornering) Share this review: Overall: 1.2 Dry 1.0 Wet 1.0 Snow 1.0 Handling 1.0 Comfort 1.0 Noise 1.0 Treadwear 5.0 295/40/20 Avoid like the plague!! Crap Crap Crap Size: 255/50R19 Vehicle: 10000 KM of Tire Wear Anonymous made this review on 6/21/2010 and is a Confident, Experienced Driver Share this review: Overall: 4.3 Dry 5.0 Wet 5.0 Snow 1.0 Handling 4.0 Comfort 4.0 Noise 1.0 Treadwear 5.0 Very noisy,can't keep balanced,edges cup really bad.Kuhmo replaced 1st set at 3000 miles because of noise and 2nd set is just as bad!! Size: Vehicle: 4827 KM of Tire Wear Anonymous made this review on 5/9/2010 and is a Aggressive Driver (Hard Cornering) Share this review: Overall: 2.4 Dry 3.0 Wet 2.0 Snow 1.0 Handling 3.0 Comfort 3.0 Noise 2.0 Treadwear 1.0 BMW X5 - 295/40RV20 106VR - Not impressed with the wear. Tires put on in Sept 09, by Feb 10 will have to replaced as it has reached its limit. Travelled less than 12000Km. Size: Vehicle: David Ford made this review on 2/3/2010 and is a Habit Not Specified Share this review: Overall: 4.2 Dry 5.0 Wet 4.0 Snow 1.0 Handling 5.0 Comfort 4.0 Noise 4.0 Treadwear 5.0 03 Infiniti FX35 AWD - 265 50R 20 - If not listed above 03 Infiniti FX35 with 265 50R 20in. After a wet fall (2x tropical storms) and definitely a snowy winter in the Southern Mid Atlantic (about 3x12 inch storms), I can confidently say these tires have exceeded my expectations. I have had to drive through pretty extreme snow conditions in the last two months, both city and highway, some rural/unmaintained. These tires bit like I never expected. Snow traction is great. Wet and ice traction is above average. Dry conditions are great. These tires are also much quiter than expected (hard on 20 in wheels) and do not seem to have worn much; the "new spikes" or whatever they are called are still visible (those little things that stick out on all new tires, maybe from the rubber injection). Sidewalls in new condition. Will rate again around 10-20k but so far, above expectations, I would recommend and certainly buy again for any of my vehicles. Size: Vehicle: Anonymous made this review on 1/31/2010 and is a Habit Not Specified Share this review: «Previous 1 2 3 4 5 6 7 8 9 10 ... Next» SpecsProduct CodeUTQG RatingSpeed RatingLoad IndexPrice 255/65R16 KL12-6376 420-A-AV109 $158.99 235/60R18 XL 2101323 420-A-AV107 $173.99 Add to Cart 255/55R18 XL KL12-6383 320-A-AV109 $180.99 Add to Cart 265/60R18 KL12-6384 420-A-AV110 $180.99 Add to Cart 275/55R18 XL 2101383 420-A-AV114 $192.99 285/60R18 KL12-6357 420-A-AV116 $182.99 Add to Cart 255/50R19 KL12-8672 420-A-AV103 $227.99 Add to Cart 285/45R19 KL12-8615 420-A-AW107 $255.99 275/45R20 KL12-8519 420-A-AW106 $166.99 Add to Cart 275/55R20 XL KL12-8328 420-A-AV117 $174.99 Add to Cart 285/50R20 KL12-8329 420-A-AV112 $182.99 Add to Cart 305/45R20 XL KL12-6490 420-A-AV116 $297.99 305/50R20 XL KL12-6489 420-A-AV120 $179.99 Add to Cart 265/35R22 XL KL12-8517 420-A-AW102 $200.99 265/40R22 XL 2101303 420-A-AV106 $216.99 285/30R22 XL KL12-7134 420-A-AW101 $339.99 * show all Advertisement


text:
Fewer than half of insurers use biometrics for cyber security: NY State financial services
The New York State Department of Financial Services published a new report that found that fewer than half of insurance providers surveyed said they use biometric solutions for cyber security, according to a report by CanadianUnderwriter.ca. Released as part of this month's "Report on Cyber Security in the Insurance Sector", New York's financial services department surveyed 43 companies including 31 health and life insurance providers and 12 property and casualty insurance providers. The report found that 58% of insurers have


text:
Welcome to
the "PENNYSPUPS" Website
We hope that you will find everything that you need here in making your decision to buy a "Lovingly Home Reared" Pedigree Beagle from us.
"PENNYSPUPS" is focused on providing high-quality service
and customer satisfaction -
we will do everything we can to meet your expectations.
LATEST NEWS: 10th February 2014
Winter is upon us! However you cannot ignore the beauty that this season offers as the days get longer towards Springtime.
"Cassiobury Park in the Winter sunshine"
**A sharp frost on Totteridge fields
Regular updates and photographs of Snowy and Penelope and
their litters will be posted on the "PENNYSPUPS" website and on our facebook page:
We hope to breed from Snowy again when she is next in season April-May with her litter due June-July and ready to leave us August- September.
We shall keep you all in the loop, of course!
was invited to appear in the Novartis Animal Health UK Onsior 2013 campaign that was created to engage both vets and pet owners with relevant information throughout their journey with the Onsior brand.
This campaign, which ranged from Veterinary Surgery waiting room posters to give away promotional packs, was also required to act as an informational tool to increase pet owner awareness of the importance appropriate exercise plays in helping to manage Osteoarthritis in their dogs.
The deployment of this campaign was monitored closely by Novartis Global and is now being successfully implemented internationally.
Penelope is still appearing on Polish TV in an Advertising campaign for CCC (footwear manufacturer in Poland) that was filmed in the Portabello Road in April 2013. Please follow this link if you would like to see the ad:
Photo Collages
of ALL our litters are posted on
"PENNYSPUPS" Our Clients and Collages
page of our website.
Valerie and I will keep you updated with the latest news from "Pennyspups" as soon as we have it.
So please flag this website as one of your bookmarks or favourites.
The most recent photographs taken of "Penelope and Snowy" and photographs of their litters are in the gallery below! Please just "click" on the photos to enlarge and to then click on the arrow if you want to start your own "slide show".
We hope to see you again! Check back soon for new updates to our website. There's much more to come!
Shakespeare's beagle
She's a beagle
true-bred, and one that adores me.
Twelfth Night,
Act 2 Scene 3 l. 172
"PENNYSPUPS" is the Kennel Name and Exclusive Breeders Signature granted by
The Kennel Club to
Mr N C Parnes and Mrs V A Parnes who are also members of
The Kennel Club Assured Breeders Scheme.
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text:
DEFINITION of 'SEC Form DEFR14A'
A form that is required to be filed with the SEC to revise definitive information previously filed in a form DEFA14A. SEC Form DEFR14A revises the additional definitive information in connection with a proxy solicitation that is filed through the latter form.
INVESTOPEDIA EXPLAINS 'SEC Form DEFR14A'
Section 14A of the code deals with notification to shareholders of matters to be brought before shareholders for a vote, and solicits proxies. DEFA14A is a filing that discloses additional definitive information in relation to that solicitation. Each change to proxy materials requires either an amendment or a revised form, as in the case of a DEFR14A.
SEC Form DEF 14AA filing with the Securities and Exchange Commission (SEC) that ...
SEC Form DEFA14AA filing with the Securities and Exchange Commission (SEC) that ...
SEC Form DEFM14AA filing with the Securities and Exchange Commission (SEC) that ...
Proxy MaterialsDocuments regulated by the Securities & Exchange Commission ...
Securities And Exchange Commission ...A government commission created by Congress to regulate the securities ...
Proxy1. An agent legally authorized to act on behalf of another party. ...
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The Impact Of Ending The US Embargo On CubaMany argue that ending the US embargo on Cuba will not only make US consumers happy, but also help the US economy and bring more freedoms to Cuba.


text: Broke my front protrac arms today and just how my luck works I can't find any till Tuesday. Was wondering if anyone has ever tried jato arms on the front of a slash 4x4 and if they are similar length. Just got all my mip axles in and can't go back to stock with arms. Any help would be appreciated


text:
16 members5 Comments 3 Likes
10 members0 Comments 0 Likes
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11 members3 Comments 1 Like
10 members1 Comment 0 Likes
Started yesterday 0 Replies 0 Likes
I just watched this CSPAN book tv discussion where Jeffery Sachs, an American economist and director of The Earth Institute at Columbia University, talks about his book 'The Age of Sustainable…Continue
Tags: sustainability, globalization, world, Jeffery-Sachs
Started this discussion. Last reply by Ina on Thursday. 4 Replies 1 Like
I subscribe to the Daily KO's, and sometimes a post is exceptionally compelling. I found this one so, and wanted to share... ~ SemileMON MAR 23, 2015 AT 09:00 AM PDT…Continue
Started this discussion. Last reply by Bonnie Smith Mar 22. 1 Reply 3 Likes
This is from the vsauce channel on youtube my son introduced me to recently. I thought it might be interesting to share here... Continue
Tags: consciousness
Started this discussion. Last reply by Jimmy G Mar 9. 4 Replies 1 Like
Humans are such an amazing species sometimes... I enjoyed this story and thought I'd share... By …Continue
Tags: monkeyman
Live your Ethics; Own your Actions; and Seek Understanding. ~ Semile 2014
All of my perceptions are limited in scope; and all of my reactions are are a result of my perceptions. ~ Theosacles 2014
Posted on December 31, 2013 at 22:05 2 Comments 4 Likes
To my galactic family watching... as another year comes to a close, and I see you in the nights sky more often than not... My message is within this 'Grassroots' song... …
Thank you for my birthday wish. I am looking forward to a relaxing day and then my roomie is taking my son and I out to a birthday dinner at my favorite restaurant. Going to be an awesome day! The only downside is I am officially a year older than I was a year ago, lol...going to start working backwards from here on! Shhhhh, don't tell.
...Good To See You Here :)....Hugz....<3
Aahaahahaha, you're right. I mixed it up. You said you know him half your life. Sorry... but the wishes remain the same.
Distraction all the way! I'm so sorry I forgot your birthday and anniversary. I think I gotta ban all the members who prevented me to post my wishes for you yesterday. Should I???
So, my very precious friend, here we go: I wish for you that you will find many moments of peace and harmony, of joy, laughter and happiness, of abundance in all areas for the new year you have just entered. And of course time to meet me in the chat room
Thank you so much Semile. Enjoy your day.


text:
Blog and News Area
Are you using F&I Training to capitalize on trends in both online shopping and subprime customers?
According to DealerTrack, 83 percent of customers are shopping for cars online. Many of those customers are spending an average of eight minutes on a dealership website calculating payments.
Some auto dealers have even taken the approach of offering customers the ability to obtain preapproval prior to coming into the dealership, providing them with immediate access to F&I. Many industry veterans, however, view the preapproval process as an outright attack on their way of doing business.
They don't want to talk numbers over the phone. They'd rather wait until the customer comes into the dealership for delivery. But waiting to discuss terms with the customer face-to-face will cause dealers to lose sales and an opportunity to secure financing.
As I see it, dealers continue to ignore the signs that more than 50 percent of consumers have nonprime to subprime credit. Or, they don't realize that to succeed in this new credit landscape, their sales and F&I personnel have to do things a little differently.
And help is readily available. My F&I training workshop – F&I Subprime Sales Success, slated for early April – targets specific challenges and provides solutions and tools for thriving in the new marketplace. For broader content, my new F&I online training platform, Chernek Consulting Virtual Pro, delivers comprehensive F&I education that uses real-world scenarios to help students grasp the lesson and put it to immediate use. This cutting-edge program – interactive, up-to-date and highly relevant – is accessible 24/7, 365 days a year. Students advance at their own pace.
Back to those subprime customers. Not properly qualifying the customer prior to landing him or her on the car cuts into profits and increases liability. Since most sales staff aren't being adequately trained to ask questions that will steer them in the right direction, customers are being put on vehicles they can't budget or get approved. The customer waits for hours in the dealership until approval is finally granted – on a different vehicle.
It's a balancing act. You don't want to offend customers with established credit, but it's the questions you don't ask that will get you into hot water every time! For example, "What brought you into our dealership today? Are you here to meet with anyone in particular? Have you purchased a vehicle from us in the past? Are you currently financing and, if so, with what bank?"
Keep in mind that you aren't interrogating the customer, you're just trying to get acquainted to better meet his or her needs. Providing the customer with the dealership's mission statement is an ideal way to frame the conversation in a positive, proactive light.
Subprime financing doesn't have to be a tug of war. If any flags are raised, bring the customer into the dealership. Obtain a credit statement and introduce the customer to the finance manager. Establishing credit criteria earlier in the process will increase the likelihood of landing the customer on the right vehicle the first time out – a vehicle the bank will buy and the customer can afford. Stripping deals down to the bare bones isn't any fun – and it's poor business sense.
Plus, vehicles are being advertised on websites with discounted pricing, but some dealers are passing the acquisition fees on to the customer – a practice that can't be defended in court. You don't want to get caught in this compliance nightmare! But that's a topic for another blog.
Tired, worn-out methods continue to plague many dealers and serve to diminish car sales and revenue. Remember, the bank decides if the customer rides. If you create a process that ensures consistency and helps to manage every sale, you'll maximize profits and overall customer satisfaction.
I created my 1½-day workshop, F&I Subprime Sales Success, to share proven methods for not only navigating the subprime marketplace, but to capitalize on its potential – while minimizing liability. This subprime training event covers:
- How to properly qualify the customer during the meet and greet.
- Understanding your banks' guidelines and procedures and knowing how to work with them.
- How to structure the deal to maximize potential.
- How to offer additional products without breaking the customer's budget or your advance.
- How to minimize liability when working with subprime customers.
Tuesday & Wednesday
April 7th & 8th
For more information or to register, go to F&I Subprime Sales Success http://www.ccilearningcenter.com/fi-subprime-sales-success.
For more comprehensive F&I training, check out Chernek Consulting Virtual Pro http://www.chernekconsultingvirtualpro.com/tour an online F&I training program that provides an interactive virtual learning experience 24/7, 365 days a year.


text:
Not Even Wrong: The Book
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Category Archives: Multiverse Mania
Back from Break
Clouds cleared about 15 minutes too late at Torshavn in the Faroe Islands, so totality was behind a cloud, but still an impressive sight. And the Faroe Islands are quite a remarkable place to visit. Some recent news: The plan … Continue reading
Posted in Multiverse Mania 22 Comments
Short Items, and a Quick Book Review
Peter Orland has a new blog, Ensnared in Vacuum, where he's writing about some non-perturbative QFT questions. Physics Today this month has book reviews of two books about theology and the multiverse (one of which I wrote about here). There … Continue reading
Posted in Book Reviews, Multiverse Mania 16 Comments
There's a very interesting new paper on the arXiv by Joe Polchinski, a survey article for Studies in History and Philosophy of Modern Physics, entitled just Dualities. It's an unusually lucid summary of the story of dualities in quantum field … Continue reading
Posted in Multiverse Mania 61 Comments
Defend the Integrity of Physics
This week's Nature features a call to arms from George Ellis and Joe Silk, entitled Scientific method: Defend the integrity of physics. I'm very glad to see well-known physicists highlighting the serious problem for the credibility of science raised by … Continue reading
Posted in Multiverse Mania 34 Comments
The Multiverse in a Nutshell
The Guardian has a podcast up today featuring Robert Trotta and David Wallace called The Multiverse in a Nutshell. It's largely more of the usual uncritical multiverse hype that has been flooding the public expositions of fundamental physics for years … Continue reading
Posted in Multiverse Mania 29 Comments
Advertisements for the Multiverse
After watching the Breakthrough Prize awards tonight, tomorrow night on the Science Channel you can watch a program that actually features physicists rather than Hollywood/Silicon Valley celebrities. There's an hour long infomercial for the Multiverse, entitled "Which Universe Are We … Continue reading
Posted in Multiverse Mania, Uncategorized 43 Comments
News, Interesting and Otherwise
On the side of interesting good news, I just heard that yet another Fields Medalist has a blog. This time it's David Mumford, who is blogging here, with his latest posting about path integrals. His website contains a wealth of … Continue reading
Posted in Experimental HEP News, Multiverse Mania, Uncategorized 7 Comments
Past the End of Science
I haven't yet seen a copy of Marcelo Gleiser's new book, but this weekend the Wall Street Journal had a review by John Gribbin, author of the 2009 multiverse-promotional effort In Search of the Multiverse. I don't know how Gleiser … Continue reading
Posted in Multiverse Mania, Uncategorized 15 Comments
Big Bang Blunder Bursts the Multiverse Bubble
This week's Nature has an article by Paul Steinhardt, with the title Big Bang blunder bursts the multiverse bubble. The subtitle of the piece describes the BICEP2 frenzy of last March as "premature hype", and the description in the body … Continue reading
Posted in Multiverse Mania 27 Comments
Quick Links
Just returned from a few days in Boston, will try and catch up here on various topics: This past week I was able to attend some of the talks at the conference in honor of David Vogan's 60th birthday. I'm … Continue reading
Posted in Langlands, Multiverse Mania, Uncategorized 9 Comments


text:
Comment: Edumacated (Score 1) 345
Full sentences harder. They verbs.
That why liberal arts and humanities important, otherwise sentences would no verbs.
We've improved Slashdot's video section; now you can view our video interviews, product close-ups and site visits with all the usual Slashdot options to comment, share, etc. No more walled garden! It's a work in progress -- we hope you'll check it out (Learn more about the recent updates).
Full sentences harder. They verbs.
That why liberal arts and humanities important, otherwise sentences would no verbs.
For n equal to one million, an O(n^2) algorithm is slower than an O(n) algorithm. Even when the O(n^2) algorithm is run in RAM, and the O(n) algorithm is disk writes being buffered and optimized by the operating system.
I'll take my Nobel Prize now, thank you.
If this magma reaches the surface it could result in lava flows.
as a computer scientist you could look into the field of evolutionary algorithms, discover that evolution is an applied science used by half of Fortune 500 companies, discover how evolution does work, and write your own code and witness first hand that evolution works.
Let's say 30% of the population are creationists.
Let's say 10% of Engineers are creationists, because creationists are less likely to pursue the field and/or because their education convinced them to no longer be creationists.
Let's say 1% of scientists are creationists, because creationists are less likely to pursue the field and/or because their education convinced them to no longer be creationists.
Result: Any creationist claiming to have a "science degree" has something like a 90% chance of turning out to have an engineering degree.... even though engineers are unlikely to be creationists.
That's the Salem Hypothesis. Creationists claiming science degrees tend to be engineers, even though engineers tend not to be creationists.
studies =shown there is no difference in effect between placebo groups and the group receiving EMF radiation
Which only goes to prove that the negative health effects of placebos can be as severe as the negative health effects caused by EMFs.
We need a law banning EMFs *and* banning placebos.
If you think organisms can't get rid of solid waste products, you must be full of shit. Chuckle.
Thank God he did this. If the GPS system had been launched we'd all be dead by now.
The denialists will still come up with an alternate interpretation of cherry-picked data from some crackpot blog, to prove you wrong.
if the same data has been used to claim a warming trend and the same data is used to say otherwise I'd call that invalid data.
The same data has been used to claim men landed on the moon, and that the moon landing was a hoax. Therefore all data related to the moon landing should then be ignored. As it's proven flawed on both counts.
earth is primarily a self regulating eco-system leading to stability
Gaia is living, breathing, self stabilizing organism. Gaia actively maintains optimum conditions for live to thrive. If the sun fluctuates hotter, Gaia will keep us cool. If the sun fluctuates cooler, Gaia will keep us warm. We have released two quadrillion pounds (2,000,000,000,000,000) of CO2 into the atmosphere and the laws of physics say that will trap heat.... and Gaia will.... umm I dunno... but Gaia will do it's super-smart-Gaia-thing to to actively counter it and keep us in a loving protective embrace of shielded stability. If we have a nuclear war, Gaia will cleanse the environment and protect us from that nasty radiation-stuff. Gaia loves all life, gaia loves us and protects us. Gaia loves broadway shows and long walks on the beach. Gaia has profiles on eHarmony.com and JDate.com.
temperatures have not significantly risen in the last 18 years.
18 year graph, yes temperatures have risen over the last 18 years.
What you were trying to cite was the was this. If you look at that graph you'll see that the earth has been on a cooling trend line (the straight lines), every year since 1965. Obviously the graph is rising, and obviously all of the cooling trend-lines are completely fictional. That's exactly how denialist websites try to quote that warming has "stopped", when it obviously hasn't. The genuine long term warming trend always breaks the fictional short-term trend lines after a few years.
When the dominant culture/language becomes decadent
Yep, American decadence is why the Soviet Union won the cold war.
10 print "pasting code on teh internets is dangerous"
20 goto 10
Please send me the full names, addresses, photos and dates of birth of all strippers in my state.
If you'd like to conserve paper you can just send the photos.
Hokey religions and ancient weapons are no substitute for a good blaster at your side. - Han Solo


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