Large VCF QUAL Values

Question

[pld]

I'm currently working on calling variants for a virus that was sequenced. For lack of a better solution, I'm using the GATK UnifiedGenotyper pipeline. I'm currently getting very large QUAL values from variants called but I'm not all that sure what to make of them.

With previous samples I've not seen any calls get QUAL values this high. The only difference I can think of is that the depth of sequencing for this sample is fairly deeper than previous ones. Has anyone else seen QUAL values this large before?

CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  subject
subject 1974    .   C   T   643225.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.995;DP=54510;Dels=0.00;ExcessHet=3.0103;FS=0.000;HaplotypeScore=1070.9305;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.104;QD=11.80;ReadPosRankSum=3.332;SOR=0.696    GT:AD:DP:GQ:PL  0/1:33593,20896:54508:99:643254,0,1131073
subject 2776    .   C   T   2282400.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=959.800;DP=668262;Dels=0.00;ExcessHet=3.0103;FS=55.352;HaplotypeScore=64018.5916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=3093.759;QD=3.42;ReadPosRankSum=517.035;SOR=9.093 GT:AD:DP:GQ:PL  0/1:566429,101157:668043:99:2282429,0,18085787
subject 2778    .   A   G   2689595.77  .   AC=1;AF=0.500;AN=2;DP=682653;Dels=0.00;ExcessHet=3.0103;FS=54.945;HaplotypeScore=57974.6917;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=3.95;SOR=6.802    GT:AD:DP:GQ:PL  0/1:572088,109628:682145:99:2689624,0,18303624
subject 3347    .   C   A   277763.77   .   AC=1;AF=0.500;AN=2;BaseQRankSum=489.237;DP=224896;Dels=0.00;ExcessHet=3.0103;FS=49.024;HaplotypeScore=11896.8305;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=914.719;QD=1.24;ReadPosRankSum=107.524;SOR=8.599  GT:AD:DP:GQ:PL  0/1:202006,22718:224896:99:277792,0,7178732

[Matthieu Miossec]

Yes, it's definitely the read depth. I didn't even know that depth of sequencing was possible.

[pld]

Viruses have very small genomes :)

Answer 1

[Zaag]

Yes I see them. Usually in multisample VCF's. The number of variant reads have a big effect on the QUAL, so the explanation probably is the higher depth in your new experiment. Further reading on QUAL: https://www.broadinstitute.org/gatk/guide/tagged?tag=QUAL

[pld]

Does this still hold for single sample VCFs?

[Zaag]

With depths of 50k, absolutely!