Hello,
I'm running GATK pipeline for Variant calling.
First starting with Bowtie2->Markduplicates->AddOrReplaceReadGroups->RealignerTargetCreator->IndelRealigner->BaseRecalibrator->PrintReads->HaplotypeCaller->GenotypeGVCFs
I've got one variant with confusing genotype call
chr5 136954583 rs4835684 T A 2126.77 VQSRTrancheSNP90.00to99.00 AC=2;AF=1.00;AN=2;DB;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.77;QD=32.89;SOR=2.428;VQSLOD=1.51;culprit=MQ GT:AD:GQ:PL 1/1:0,57:99:2155,171,0
Here it is showing AD 0,57 and it's 1/1 genotype, but when I checked manually in samtools viewer there are 33(T) REF calls and 22(A) ALT calls. I don't understand why 1/1 genotype called by HaplotypeCaller?
Then to confirm this variant I ran HaplotypeCaller with -bamout option, as suggested in this thread https://gatkforums.broadinstitute.org/gatk/discussion/5042/genotype-calling-in-gatk.
When I viewed output of -bamout in samtools tview it's showing all ALT(A) calls. I think HaplotypeCaller is performing some steps which I'm not understanding. But how come ALT calls got increased in -bamout output. Am I missing something?
I'm totally confused.
Please help. Any help would be appreciated!! Thanks