If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
VQST error with no DP annotation
Based on GATK document, I have successfully generated raw vcf file. Now I am trying to to the "Variant Quality Score Recalibration (VQSR)" procedure before the annotation.
For this, variantRecalibrator procedure should have been done. For SNP calibaration,
java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R genome.fa -input 1-WMT.vcf
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ./dbsnp_138.hg19.vcf -an DP -an QD -an FS -an MQRankSum -mode SNP -recalFile raw.SNPs.recal -tranchesFile raw.SNPs.tranches -rscriptFile recal.plots.
I have continuously had errors saying that " Values for DP annotation not detected for ANY training variant " " Values for QD annotation not detected for ANY training variant " " Values for FS annotation not detected for ANY training variant ". Even though my input.raw.vcf file has those annotations..
.chrM 150 . T C 13548.77 . AC=2;AF=1.00;AN=2;DP=473;FS=0.000;GQ_MEAN=1419.00;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;NCC=0;QD=28.64;SOR=1.344 GT:AD: DP:GQ:PL 1/1:0,473:473:99:13577,1419,0
chrM 195 . C T 15178.77 . AC=2;AF=1.00;AN=2;DP=521;FS=0.000;GQ_MEAN=1562.00;MLEAC=2;MLEAF=1.00;MQ=40.43;MQ0=0;NCC=0;QD=29.13;SOR=0.890 GT:AD: DP:GQ:PL 1/1:0,521:521:99:15207,1562,0
I have also tested the comparison of vcf file with goldstandard and my vcf file.
The big difference in my case is that there are no overlap.. since currently I am starting with only mitochondira genes. So, my vcf file only have about 44 snps which has no overlap with hapmap vcf file. I have tested with other traning set. most of them do not have an overlap.. Sometime only 1 snps overlap with
I am not sure whether it is a problem or not.
Such case which do not have overlappped snps, can I still apply VariantCalibrator step?