Hi all,
I have used bcftools to filter the variants on my WES dataset with the
below shown parameters:
vcfutils.pl varFilter -Q 40 -d 10 -a 10 SamSNP.vcf | awk '$6<=30'
In detail, RMSmapping quality, Q 40
minimum depth 10
minimum reads for alternate base 10
and then QUAL<=30
Then i tried to investigate the resulting variants which are shown below:
chr1 18440259 . A G 24 .
DP=41;VDB=3.198325e-03;RPB=-2.855659e+00;AF1=0.5;AC1=1;DP4=17,11,11,0;MQ=53;FQ=27;PV4=0.017,1.2e-08,2e-37,1
GT:PL:GQ 0/1:54,0,242:57
chr1 78618486 . T C 8.64 .
DP=62;VDB=1.595146e-01;RPB=-8.823841e-01;AF1=0.5;AC1=1;DP4=3,37,2,16;MQ=46;FQ=11.3;PV4=0.64,1,7.8e-21,0.3
GT:PL:GQ 0/1:38,0,192:40
chr1 84078188 . G A 6.98 .
DP=71;VDB=8.165945e-03;RPB=7.733564e-01;AF1=0.4999;AC1=1;DP4=21,30,11,9;MQ=52;FQ=9.53;PV4=0.43,0.21,2.3e-36,1
GT:PL:GQ 0/1:36,0,255:37
chr1 84078211 . T C 9.52 .
DP=68;VDB=7.138134e-03;RPB=3.693204e+00;AF1=0.5;AC1=1;DP4=16,32,10,9;MQ=52;FQ=12.3;PV4=0.17,1,9.9e-34,1
GT:PL:GQ 0/1:39,0,255:41
chr1 84078212 . G A 8.64 .
DP=67;VDB=7.138134e-03;RPB=3.894576e+00;AF1=0.5;AC1=1;DP4=16,31,10,9;MQ=52;FQ=11.3;PV4=0.18,0.015,3.6e-33,1
GT:PL:GQ 0/1:38,0,255:40
chr1 84078223 . C A 4.77 .
DP=62;VDB=1.658616e-03;RPB=3.810234e+00;AF1=0.4999;AC1=1;DP4=16,30,9,6;MQ=53;FQ=6.99;PV4=0.13,0.0041,1.1e-30,0.0018
GT:PL:GQ 0/1:33,0,255:33
chr1 102442684 . A C 30 .
DP=80;VDB=2.593477e-02;RPB=2.321748e+00;AF1=0.5;AC1=1;DP4=9,49,0,19;MQ=51;FQ=33;PV4=0.1,1,3.1e-15,0.39
GT:PL:GQ 0/1:60,0,229:63
Despite the QUAL value is less than 30, most of the variants have good
coverage. I wonder how these variants should be treated. Could someone
comment on this behaviour to get a better understanding whether to
discard or retain these variants.
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