Tagged with #variantannotator annotations
31 documentation articles | 0 announcements | 6 forum discussions



Created 2012-07-23 23:57:01 | Updated 2012-07-23 23:57:01 | Tags: transmissiondisequilibriumtest gatkdocs
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A new tool has been released!

Check out the documentation at TransmissionDisequilibriumTest.


Created 2012-07-23 23:56:59 | Updated 2012-07-23 23:56:59 | Tags: tandemrepeatannotator gatkdocs
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A new tool has been released!

Check out the documentation at TandemRepeatAnnotator.


Created 2012-07-23 23:56:56 | Updated 2012-07-23 23:56:56 | Tags: spanningdeletions gatkdocs
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A new tool has been released!

Check out the documentation at SpanningDeletions.


Created 2012-07-23 23:56:54 | Updated 2012-07-23 23:56:54 | Tags: snpeff gatkdocs
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A new tool has been released!

Check out the documentation at SnpEff.


Created 2012-07-23 23:56:47 | Updated 2012-07-23 23:56:47 | Tags: samplelist gatkdocs
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A new tool has been released!

Check out the documentation at SampleList.


Created 2012-07-23 23:56:38 | Updated 2012-07-23 23:56:38 | Tags: readposranksumtest gatkdocs
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A new tool has been released!

Check out the documentation at ReadPosRankSumTest.


Created 2012-07-23 23:56:32 | Updated 2012-07-23 23:56:32 | Tags: rmsmappingquality gatkdocs
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A new tool has been released!

Check out the documentation at RMSMappingQuality.


Created 2012-07-23 23:56:30 | Updated 2012-07-23 23:56:30 | Tags: qualbydepth gatkdocs
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A new tool has been released!

Check out the documentation at QualByDepth.


Created 2012-07-23 23:56:19 | Updated 2012-07-23 23:56:19 | Tags: nbasecount gatkdocs
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A new tool has been released!

Check out the documentation at NBaseCount.


Created 2012-07-23 23:56:09 | Updated 2012-07-23 23:56:09 | Tags: mappingqualityzerofraction gatkdocs
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A new tool has been released!

Check out the documentation at MappingQualityZeroFraction.


Created 2012-07-23 23:56:08 | Updated 2012-07-23 23:56:08 | Tags: mappingqualityzerobysample gatkdocs
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A new tool has been released!

Check out the documentation at MappingQualityZeroBySample.


Created 2012-07-23 23:56:07 | Updated 2012-07-23 23:56:07 | Tags: mappingqualityzero gatkdocs
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A new tool has been released!

Check out the documentation at MappingQualityZero.


Created 2012-07-23 23:56:06 | Updated 2012-07-23 23:56:06 | Tags: mappingqualityranksumtest gatkdocs
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A new tool has been released!

Check out the documentation at MappingQualityRankSumTest.


Created 2012-07-23 23:56:03 | Updated 2012-07-23 23:56:03 | Tags: mvlikelihoodratio gatkdocs
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A new tool has been released!

Check out the documentation at MVLikelihoodRatio.


Created 2012-07-23 23:56:02 | Updated 2012-07-23 23:56:02 | Tags: lowmq gatkdocs
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A new tool has been released!

Check out the documentation at LowMQ.


Created 2012-07-23 23:55:57 | Updated 2012-07-23 23:55:57 | Tags: indeltype gatkdocs
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A new tool has been released!

Check out the documentation at IndelType.


Created 2012-07-23 23:55:55 | Updated 2012-07-23 23:55:55 | Tags: inbreedingcoeff gatkdocs
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A new tool has been released!

Check out the documentation at InbreedingCoeff.


Created 2012-07-23 23:55:54 | Updated 2012-07-23 23:55:54 | Tags: homopolymerrun gatkdocs
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A new tool has been released!

Check out the documentation at HomopolymerRun.


Created 2012-07-23 23:55:53 | Updated 2012-07-23 23:55:53 | Tags: heteroplasmy gatkdocs
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A new tool has been released!

Check out the documentation at Heteroplasmy.


Created 2012-07-23 23:55:52 | Updated 2012-07-23 23:55:52 | Tags: hardyweinberg gatkdocs
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A new tool has been released!

Check out the documentation at HardyWeinberg.


Created 2012-07-23 23:55:52 | Updated 2012-07-23 23:55:52 | Tags: haplotypescore gatkdocs
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A new tool has been released!

Check out the documentation at HaplotypeScore.


Created 2012-07-23 23:55:47 | Updated 2012-07-23 23:55:47 | Tags: gccontent gatkdocs
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A new tool has been released!

Check out the documentation at GCContent.


Created 2012-07-23 23:55:44 | Updated 2012-07-23 23:55:44 | Tags: fisherstrand gatkdocs
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A new tool has been released!

Check out the documentation at FisherStrand.


Created 2012-07-23 23:55:29 | Updated 2013-04-12 03:10:39 | Tags: depthofcoverage gatkdocs
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A new tool has been released!

Check out the documentation at DepthOfCoverage.


Created 2012-07-23 23:55:29 | Updated 2012-07-23 23:55:29 | Tags: depthperallelebysample gatkdocs
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A new tool has been released!

Check out the documentation at DepthPerAlleleBySample.


Created 2012-07-23 23:55:10 | Updated 2012-07-23 23:55:10 | Tags: clippingranksumtest gatkdocs
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A new tool has been released!

Check out the documentation at ClippingRankSumTest.


Created 2012-07-23 23:55:08 | Updated 2012-07-23 23:55:08 | Tags: chromosomecounts gatkdocs
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A new tool has been released!

Check out the documentation at ChromosomeCounts.


Created 2012-07-23 23:55:00 | Updated 2012-07-23 23:55:00 | Tags: basequalityranksumtest gatkdocs
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A new tool has been released!

Check out the documentation at BaseQualityRankSumTest.


Created 2012-07-23 23:54:59 | Updated 2012-07-23 23:54:59 | Tags: basecounts gatkdocs
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A new tool has been released!

Check out the documentation at BaseCounts.


Created 2012-07-23 23:54:47 | Updated 2012-07-23 23:54:47 | Tags: allelebalance gatkdocs
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A new tool has been released!

Check out the documentation at AlleleBalance.


Created 2012-07-23 23:54:47 | Updated 2012-07-23 23:54:47 | Tags: allelebalancebysample gatkdocs
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A new tool has been released!

Check out the documentation at AlleleBalanceBySample.

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Created 2015-02-11 21:42:59 | Updated | Tags: haplotypecaller
Comments (7)

Hi,

We are running the best practices pipeline for variant discovery with GATK 3-2.2. When running the HaplotypeCaller with the flags -A AlleleBalance & -A HomopolymerRun to generate a gVCF, there are no ABHet/ABHom or HRun annotations showing up in the gVCF. I tried running VariantAnnotator on the gVCF and still no annotations.

The documentation on both of these annotations state that they only work for biallelic variants. I suspected that the , tag that is on every variant might be causing the tool to treat biallelic variants as multiallelic. So I stripped the , from the gVCF using sed and reran the VariantAnnotator and voila...I got the annotations.

Is there a way to either generate the gVCF without the , tag (and probabilities that go with it), or instruct the VariantAnnotator to ignore the , tag.

Thanks for you help.

Tom Kolar


Created 2014-12-11 15:57:03 | Updated | Tags: haplotypecaller variantannotator
Comments (4)

Hello

I am using GATK 3.3-0 HaplotypeCaller for variant calling. When I run HaplotypeCaller with the command

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R all_chr_reordered.fa -I 30_S30.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 50 -o 30_S30_control1.vcf -L brca.intervals

I get all the variants I want, however, I also want to get the number of forward and reverse reads that support REF and ALT alleles. Therefore I use StrandBiasBySample annotation when running HaplotypeCaller with the command:

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R all_chr_reordered.fa -I 30_S30.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 50 -o 30_S30_control2.vcf -L brca.intervals -A StrandBiasBySample

The SB field is added, but a variant that was in 30_S30_control1.vcf is absent in 30_S30_control2.vcf. All the remaining variants are there. The only difference between two variant calls was adding -A StrandBiasBySample. What I'm wondering about is that why this one variant is absent.

the missing variant: 17 41276152 . CAT C 615.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;ClippingRankSum=0.564;DP=639;FS=15.426;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.054;QD=0.96;ReadPosRankSum=0.698;SOR=2.181 GT:AD:DP:GQ:PL 0/1:565,70:635:99:653,0,18310

So I decided to run HaplotypeCaller without -A StrandBiasBySample and later add the annotations with VariantAnnotator. Here is the command:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R all_chr_reordered.fa -I 30_S30.bam --variant 30_S30_control1.vcf -L 30_S30_control1.vcf -o 30_S30_control1_SBBS.vcf -A StrandBiasBySample

However, the output vcf file 30_S30_control1_SBBS.vcf was not different from the input variant file 30_S30_control1.vcf except for the header, SB field wasn't added. Why was the SB field not added? Is there any other way to get the number of forward and reverse reads?

Please find 30_S30_control1.vcf, 30_S30_control2.vcf and 30_S30_control1_SBBS.vcf in attachment

Thanks


Created 2013-12-08 21:55:56 | Updated 2013-12-08 22:02:48 | Tags:
Comments (4)

Hey, GATK team,

I downloaded snpEff and browsed the database by inputting the commands as $ java -jar snpEff.jar databases

It provides a list of database of all available species including mouse's as follows (GRCm38.73 )

http://sourceforge.net/projects/snpeff/files/databases/v3.4/snpEff_v3.4_Mus_musculus.zip

However, there is no database of GRCm38 under the actual databases at all.

Did I missed something or database is still under construction? Where can I download the mouse database? I need to do functional annotation of my variant VCF file.

In addition, according to the presentation materials in GATK, we will do variant filter/selectvariant right after annotation, or it does not matter which one goes first?

Thanks


Created 2013-07-23 19:44:06 | Updated | Tags: variantannotator vcf genotype annotation
Comments (9)

Hi,

Could you tell me how to encourage GATK to annotate my genotype columns (i.e. add annotations to the FORMAT and PANC_R columns in the following file):

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PANC_R 
chrX 259221 . GA G 136.74 . AC=2;AF=1.00;AN=2;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=8.82;MQ0=1;QD=3.04 GT:AD:GQ:PL 1/1:0,2:6:164,6,0

The file was generated with HaplotypeCaller. I used a command line similar to this one to no effect:

java -jar $GATKROOT/GenomeAnalysisTK.jarT VariantAnnotator -R hg19_random.fa -I chr7_recalibrated.bam -V chr7.vcf --dbsnpdbSNP135_chr.vcf -A Coverage -A QualByDepth -A FisherStrand -A MappingQualityRankSumTest -A ReadPosRankSumTest -o chr7_annotated-again.vcf

Does anyone have any suggestions? Thanks in advance!


Created 2013-04-30 12:45:05 | Updated 2013-04-30 12:45:25 | Tags: variantrecalibrator combinevariants variantannotator annotations
Comments (4)

I have a set of VCFs with identical positions in them:

VCF1: 1 10097 . T . 26 . AN=196;DP=1622;MQ=20.06;MQ0=456 GT:DP

VCF2: 1 10097 . T . 21.34 . AN=198;DP=2338;MQ=19.53;MQ0=633 GT:DP

VCF3: 1 10097 . T . 11.70 . AN=240;DP=3957;MQ=19.74;MQ0=1085 GT:DP

VCF4: 1 10097 . T . 15.56 . AN=134;DP=1348;MQ=18.22;MQ0=442 GT:DP

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.


Created 2012-11-19 02:07:53 | Updated | Tags: mappingqualityranksumtest readposranksumtest variantannotator
Comments (11)

Hi,

I'm attempting to use Variant Annotator to annotate some VCFs produced by samtools so I can run VQSR on them. Unfortunately I've gottent stuck and I'm trying to figure out why Variant Annotator wouldn't be annotating INDELs with MappingQualityRankSumTest and ReadPosRankSumTest, it seems to annotate SNPs fine. There are both Homs and het's called on the sample. Could it be I need to left align the indels to get enough coverage? What would you suggest is the best way to debug this? Is there a way to make GATK behave more verbosely about why it's refusing an annotation?

Thanks Martin