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.
select intersection, merged VCF files
I am using GATK3 and trying to compare two samples. I have a merged vcf file of two samples.
I tried running below protocol.
java -jar GenomeAnalysisTK.jar -T SelectVariants \ -R hg19.fasta \ -V C01.vcf \ -select 'set == "Intersection";’ \ -o C01._invertselect.vcf \ -invertSelect
I got invertselect files, but it detected not only the difference of genotype. It detected the difference of filtered depth, too.
chr1 12783 . G A 341.69 PASS AC=4;AF=1;AN=4;DP=304;FS=0;MQ=12.58;MQRankSum=1.953;QD=1.12;ReadPosRankSum=2.964;SOR=2.584 GT:AD:AF:DP:GP:GQ:PL 1/1:10,39:0.796:49:29.36,15.36,0.1334:15:67,18,0 1/1:10,39:0.796:49:29.09,15.09,0.1421:15:67,18,0
How can i detect the difference of only genotype ?
I do appreciate your help.