By default, we trust PASS filters on VCF files. If a VCF is not filtered or PASS filters are not present, we use a very basic universal filter that relies on QUAL (Quality) and DP (Depth), which is better than nothing. If you want to run all of your data through GenVue Discovery regardless of quality, you or your provider must put PASS filters on all variants in your VCF file. I have us.dantelabs.com file hg19 /GRCh37
**291.raw.vcf**
##fileformat=VCFv4.2
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
#contig=<ID=hs37d5,length=35477943>
##reference=file:///references/grch37/reference.bin
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 291
1 10177 . A AC 43.52 . AC=1;AF=0.500;AN=2;DP=114;FS=13.306;MQ=25.21;MQRankSum=-2.232;QD=0.38;ReadPosRankSum=1.146;SOR=0.617;FractionInformativeReads=0.658;R2_5P_bias=-17.815 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:15,60:0.800:75:3,32:12,28:6:44,0,1:4.3520e+01,1.3955e+00,5.6103e+00:0.00,2.00,5.00:11,4,26,34:7,8,28,32
1 10230 . AC A 42.13 . AC=1;AF=0.500;AN=2;DP=122;FS=10.543;MQ=25.94;MQRankSum=-1.250;QD=0.35;ReadPosRankSum=1.088;SOR=1.888;FractionInformativeReads=0.672;R2_5P_bias=4.813 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:32,50:0.610:82:18,24:14,26:37:72,0,35:4.2129e+01,9.0222e-04,3.8342e+01:0.00,30.00,33.00:14,18,12,38:16,16,28,22
1 10247 . TA T 28.14 . AC=1;AF=0.500;AN=2;DP=110;FS=2.032;MQ=27.83;MQRankSum=0.279;QD=0.26;ReadPosRankSum=1.158;SOR=1.042;FractionInformativeReads=0.709;R2_5P_bias=6.131 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:49,29:0.372:78:26,14:23,15:28:63,0,46:2.8143e+01,6.7236e-03,4.8757e+01:0.00,35.00,38.00:19,30,9,20:28,21,12,17
1 10254 . TA T 42.11 . AC=1;AF=0.500;AN=2;DP=110;FS=4.298;MQ=27.96;MQRankSum=-0.433;QD=0.38;ReadPosRankSum=1.726;SOR=1.207;FractionInformativeReads=0.755;R2_5P_bias=-18.055 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:41,42:0.506:83:23,18:18,24:41:77,0,46:4.2107e+01,3.2540e-04,4.8750e+01:0.00,35.00,38.00:18,23,14,28:22,19,20,22
1 10285 . T C 33.09 . AC=1;AF=0.500;AN=2;DP=132;FS=5.110;MQ=22.46;MQRankSum=1.791;QD=0.25;ReadPosRankSum=3.403;SOR=1.415;FractionInformativeReads=0.545;R2_5P_bias=-9.574 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB
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