vcfutils.pl varFilter removes INDELs even with default override

[hansdd]

Dear All,

I am running vcfutils.pl varFilter and I have deliberately set all options to very low values to override the defaults so no filtering occurs. Command here:

samtools-0.1.18/bcftools/vcfutils.pl varFilter -Q0 -d0 -D10000000 -a 0 -1 0 -2 0 -3 0 -4 0 -w0 -W0 -e0 IN.vcf > OUT.vcf

However, this still removes some variants. I have not been able to determine why these variants are removed. They are mostly INDELs.

Does anyone have an idea why these are removed?

A sample of them is below:

Chr29 46196908 . C CA 999 . INDEL;DP=843;VDB=0.0280;AF1=0.1837;G3=0.633,0.367,2.782e-06;HWE=0.0137;AC1=49;DP4=329,373,23,50;MQ=43;FQ=999;PV4=0.013,1,5e-07,5.9e-07 GT:PL:GQ
Chr29 46197067 . CT C 66.4 . INDEL;DP=416;VDB=0.0253;AF1=0.8572;AC1=228;DP4=1,0,0,6;MQ=39;FQ=-17.2;PV4=0.14,1,1,0.036 GT:PL:GQ
Chr29 46197249 . G A 138 . DP=102;VDB=0.0148;AF1=0.1197;AC1=32;DP4=52,35,10,0;MQ=53;FQ=139;PV4=0.012,1,1,0.027 GT:PL:GQ
Chr29 46201663 . ACAC A 16.4 . INDEL;DP=712;VDB=0.0296;AF1=0.03825;AC1=10;DP4=252,139,12,5;MQ=54;FQ=16.6;PV4=0.8,5.3e-10,1,1 GT:PL:GQ
Chr29 46201672 . CACACACA CACACACATACACACA 999 . INDEL;DP=729;VDB=0.0320;AF1=0.1679;G3=0.647,0.353,1.629e-07;HWE=0.0375;AC1=44;DP4=208,150,43,16;MQ=53;FQ=999;PV4=0.032,1,0.015,1 GT:PL:GQ
Chr29 46216656 . GAC GC 999 . INDEL;DP=751;VDB=0.0324;AF1=0.2325;G3=0.7493,0.05407,0.1966;HWE=0.0115;AC1=62;DP4=37,29,16,20;MQ=59;FQ=999;PV4=0.3,1.9e-09,1,1 GT:PL:GQ
Chr29 46226316 . TGTGTGTGTGCG TG 999 . INDEL;DP=549;VDB=0.0276;AF1=0.257;AC1=68;DP4=33,85,30,33;MQ=50;FQ=999;PV4=0.0093,0.00039,1,0.0067 GT:PL:GQ
Chr29 46226318 . TGTGTGTGCG TG 999 . INDEL;DP=554;VDB=0.0276;AF1=0.5859;AC1=156;DP4=16,47,53,95;MQ=47;FQ=999;PV4=0.15,1,0.33,1 GT:PL:GQ
Chr29 46226322 . TGTGCGCG TGCG 999 . INDEL;DP=77;VDB=0.0247;AF1=0.3246;AC1=86;DP4=3,7,5,4;MQ=40;FQ=999;PV4=0.37,1,1,1 GT:PL:GQ
Chr29 46247847 . G A 999 . DP=1452;VDB=0.0331;AF1=0.6119;AC1=163;DP4=190,145,241,196;MQ=56;FQ=999;PV4=0.71,2e-280,1,1 GT:PL:GQ
Chr29 46247847 . GAAAAA GAAAAAA 999 . INDEL;DP=1452;VDB=0.0331;AF1=0.1274;AC1=34;DP4=498,389,84,52;MQ=57;FQ=999;PV4=0.23,1,5.3e-37,0.024 GT:PL:GQ
Chr29 46264295 . AG AGG 93.3 . INDEL;DP=696;VDB=0.0277;AF1=0.5368;AC1=143;DP4=0,9,4,5;MQ=35;FQ=50.7;PV4=0.082,0.012,1,1 GT:PL:GQ
Chr29 46264351 . ATG A 999 . INDEL;DP=263;VDB=0.0105;AF1=1;AC1=266;DP4=0,0,0,13;MQ=57;FQ=-32.6 GT:PL:GQ
Chr29 46273882 . CAAAAAAAAA CAAAAAAAA 66.2 . INDEL;DP=951;VDB=0.0334;AF1=0.1236;AC1=33;DP4=134,200,31,61;MQ=58;FQ=66.7;PV4=0.28,0.029,0.04,1 GT:PL:GQ
Chr29 46273891 . A T 13.1 . DP=890;VDB=0.0267;AF1=0.0655;G3=0.9164,0.007097,0.07654;HWE=0.0498;AC1=17;DP4=135,232,4,19;MQ=58;FQ=13.3;PV4=0.073,4.1e-31,0.28,1 GT:PL:GQ
Chr29 46277700 . GAAAAAAAAAAAAAAAA GAAAAAAAAAAAAAAA 64.2 . INDEL;DP=587;VDB=0.0276;AF1=0.6356;G3=0.4456,0.0001152,0.5542;HWE=5.96e-07;AC1=169;DP4=59,40,120,88;MQ=59;FQ=-3.7;PV4=0.8,1,1,1 GT:PL:GQ
Chr29 46279336 . N NA 999 . INDEL;DP=175;VDB=0.0016;AF1=1;AC1=266;DP4=0,0,175,0;MQ=29;FQ=-37 GT:PL:GQ
Chr29 46291817 . TGGG TGG 999 . INDEL;DP=671;VDB=0.0318;AF1=0.2592;G3=0.6341,0.225,0.1409;HWE=0.0377;AC1=69;DP4=103,59,75,48;MQ=59;FQ=999;PV4=0.71,2.3e-09,0.36,1 GT:PL:GQ
Chr29 46303811 . G C 999 . DP=909;VDB=0.0292;AF1=0.6786;G3=0.1878,0.2743,0.5379;HWE=0.0047;AC1=181;DP4=129,121,296,260;MQ=59;FQ=999;PV4=0.7,1.7e-12,1,1 GT:PL:GQ
Chr29 46368746 . CTTCGGGCGT CT 35.9 . INDEL;DP=87;VDB=0.0255;AF1=0.183;AC1=48;DP4=22,47,4,2;MQ=58;FQ=36.8;PV4=0.17,0.0098,2.1e-16,2.7e-06 GT:PL:GQ
Chr29 46391702 . GCAA GAA 27.9 . INDEL;DP=303;VDB=0.0245;AF1=0.05679;AC1=15;DP4=141,58,3,15;MQ=58;FQ=28.1;PV4=8.9e-06,0.00081,1,0.3 GT:PL:GQ