Hi,
I'm trying to filter out variants in a .vcf file that I generated from DNAseq data (BWA->picard->GATK).
I'm following the most recent documentation I can find on VariantFiltration and the most basic command:
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R genome.fa -V raw_snps.vcf -o filtered_snp.vcf --filterExpression "QD < 10.0" --filterName "my_snp_filter"
This throws no errors but filters out nothing. I've been fighting with this for several days now (after I realized that this step in my pipeline was failing).
Apparently my university's cluster only has GATK 3.6 installed--could that be the problem?
I'll paste a couple of lines form my input .vcf to see if that file looks correctly formatted (was generated via HaplotypeCaller):**_``_**.
X 23538706 . A T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068e+00;ClippingRankSum=0.00;DP=15;ExcessHet=3.0103;FS=9.859;MLEAC=1;MLEAF=0.500;MQ=48.55;MQRankSum=-3.239e+00;QD=10.72;ReadPosRankSum=-1.964e+00;SOR=3.556 GT:AD:DP:GQ:PGT:PID:PL 0/1:9,6:15:99:0|1:23538706_A_T:189,0,353
X 23538720 . T A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.147e+00;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.932;MLEAC=1;MLEAF=0.500;MQ=51.53;MQRankSum=-2.467e+00;QD=5.65;ReadPosRankSum=-2.362e+00;SOR=1.828 GT:AD:DP:GQ:PGT:PID:PL 0/1:9,3:12:96:0|1:23538706_A_T:96,0,408
X 23538721 . G T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000e+00;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.932;MLEAC=1;MLEAF=0.500;MQ=51.53;MQRankSum=-2.467e+00;QD=5.65;ReadPosRankSum=-2.838e+00;SOR=1.828 GT:AD:DP:GQ:PGT:PID:PL 0/1:9,3:12:96:0|1:23538706_A_T:96,0,408
Thank you for any help!