BaseQRankSum and FS

Question

[Tania]

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

Answer 1

[miaowzai]

I haven't seen anyone using these two values for hard filtering. But BaseQRankSum is basically a z-score for base qualities of reference and alternative alleles. Having a BaseQRankSum close to 0 means the reference and alternative alleles have the same base qualities and having BaseQRankSum around 2 means they differ by 2 SDs (positive 2 means alternative alleles have higher qualities). If this value is away from 0, there's probably some sequencing bias. I don't know much detail about that. I'm guessing you could use either 0.5, 1, 1.5, 2 as the cutoff for this value, depending on how strict your filtering is and how many loci are left after your filtering. Reference: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_BaseQualityRankSumTest.php

FS means fisher strand. It is another measure of sequencing bias. It measures in squencing if one strand is preferred than the other one. Larger values means larger bias. I suggest you extract all your FS and plot them in a histogram and choose a cutoff depending on how many loci you'd like to retain. Reference: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_FisherStrand.php

[jena]

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).