Fix a problem which causes false negative I've been using Lancet to call variants from target capture data and noticed one SOMATIC short tandem repeat be filtered by HighVafNormal;HighAltCntNormal with WRONG normal AD which can be detected by Varscan2/Mutect2.
Before (commit=ce36626c2bb)
lancet vcf(fn)
CHROM
POS
ID
REF
ALT
QUAL
FILTER
INFO
FORMAT
normal
tumor
chr17
37880984
.
A
ATACGTGATGGCT
1119.11
HighVafNormal;HighAltCntNormal
SHARED;FETS=1119.11;TYPE=ins;LEN=12;KMERSIZE=17;SB=14.2495
GT:AD:SR:SA:DP
0/1:2101,811:1292,809:2,809:2912
0/1:4001,346:2159,1842:181,165:4347
varscan2 vcf(tp)
CHROM
POS
ID
REF
ALT
QUAL
FILTER
INFO
FORMAT
normal
tumor
chr17
37880984
.
A
ATACGTGATGGCT
.
PASS
DP=4227;SOMATIC;SS=2;SSC=250;GPV=1E0;SPV=8.049E-26
GT:GQ:DP:RD:AD:FREQ:DP4
0/0:.:1387:1387:0:0%:1068,319,0,0
0/1:.:2840:2691:142:5.01%:2287,404,116,26
mutect2 vcf(tp)
CHROM
POS
ID
REF
ALT
QUAL
FILTER
INFO
FORMAT
normal
tumor
chr17
37880984
.
A
ATACGTGATGGCT
.
.
AS_SB_TABLE=2424,2071|149,149;DP=5352;ECNT=1;MBQ=20,20;MFRL=172,154;MMQ=60,60;MPOS=38;NALOD=3.18;NLOD=348.86;POPAF=6.00;RPA=1,2;RU=TACGTGATGGCT;STR;TLOD=980.44
GT:AD:AF:DP:F1R2:F2R1:SB
0/0:1402,0:8.283e-04:1402:713,0:677,0:815,587,0,0
0/1:3093,298:0.088:3391:1660,131:1422,134:1609,1484,149,149
CHROM
POS
ID
REF
ALT
QUAL
FILTER
INFO
FORMAT
normal
tumor
chr17
37880984
.
A
ATACGTGATGGCT
437.116
PASS
SOMATIC;FETS=437.116;TYPE=ins;LEN=12;KMERSIZE=25;SB=15.3947
GT:AD:SR:SA:DP
0/0:1463,0:875,588:0,0:1463
0/1:3897,327:2110,1787:168,159:4224