How is GT determined in vardict? #186
Description
Hello!
I found this piece of code from var2vcf_valid on how to determine GT:
$gt = (1-$af < $GTFreq) ? "1/1" : ($af >= 0.5 ? "1/0" : ($af >= $Freq ? "0/1" : "0/0"))
The output of my VCF has this result:
chr13 32907420 . GA G 201 PASS ADJAF=0.0023;AF=0.0118;BIAS=2:2;DP=5184;HIAF=0.0118;HICNT=61;HICOV=5161;LSEQ=TGATGAAACATCTTATAAAG;MQ=60;MSI=8;MSILEN=1;NM=0.1;ODDRATIO=1.12694;PMEAN=16.5;PSTD=1;QSTD=1;QUAL=34;REFBIAS=2588:2534;RSEQ=AAAAAAATACCGAAAGACCA;SAMPLE=Sample_cap56_hm_equinox_4.deduped;SBF=0.69988;SHIFT3=7;SN=122;TYPE=Deletion;VARBIAS=29:32;VD=61 GT:DP:VD:AD:AF:RD:ALD 0/1:5184:61:5122,61:0.0118:2588,2534:29,32
Based on the script, the GT for this variant should be 0/0, right? Or am I missing something here?
Thanks!