Hi All
Can anyone give me a roughly cutoff for BaseQRankSum and FS in vcf? I need to know a hint about what is too low to accept or what is a good? Something like this, I can't interpret:
BaseQRankSum=1.875;DP=1987;Dels=0.00;FS=3.500;HaplotypeScore=1.1051;InbreedingCoeff=-0.0043;MLEAC=3;MLEAF=0.019;MQ0=1;MQ=58.73;MQRankSum=0.871;QD=13.15;ReadPosRankSum=-0.989;SOR=1.630 GT:AD:DP:GQ:PL 0/1:7,14:21:99:383,0,139
Thanks
It should be noted that BaseQRankSum can be negative (when reference base has higher quality than alternative). So if you are considering cutoffs, you should also account for the negative values (e.g. cutoff 1 & -1).