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.