indel read count

[noe91]

Hello!

I am using Strelka as variant caller for INDELs. I would like to obtain the number of read supporting the REF and the ALT for tumor and normal sample pairs.

I have found in the documentation:

tier1RefCounts = First comma-delimited value from FORMAT/TAR
tier1AltCounts = First comma-delimited value from FORMAT/TIR
Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)

But I always have for the normal sample a TIR=0 and for tumor sample a TAR=0.  I reported here the first lines of my vcf:

chr4    119176585       .       CTG     C       .       PASS    IC=0;IHP=2;NT=ref;QSI=41;QSI_NT=40;RC=1;RU=TG;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1     DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   3:3:3,3:0,0:0,0:4.68:0.00:0.00  29:29:0,0:27,27:2,2:29.52:0.35:0.00
chr12   30887814        .       ACACACACT       A       .       PASS    IC=0;IHP=2;NT=ref;QSI=41;QSI_NT=41;RC=1;RU=CACACACT;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1       DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   6:6:7,8:0,0:1,0:10.03:0.21:0.00 17:17:0,0:16,16:2,2:22.46:0.19:0.00
chr14   22694510        .       CTGTGTCCGTG     C       .       PASS    IC=0;IHP=2;NT=ref;QSI=40;QSI_NT=40;RC=1;RU=TGTGTCCGTG;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1     DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   4:4:4,4:0,0:0,0:3.87:0.00:0.00  19:19:0,0:19,20:0,0:19.6:0.00:0.00
chr14   71513930        .       TG      T       .       PASS    IC=0;IHP=2;NT=ref;QSI=40;QSI_NT=39;RC=1;RU=G;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1      DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   5:5:5,5:0,0:0,0:5.94:0.00:0.00  18:18:0,0:18,18:0,0:20.5:0.00:0.00
chr15   41246237        .       A       ATC     .       PASS    IC=1;IHP=2;NT=ref;QSI=40;QSI_NT=40;RC=0;RU=TC;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1     DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   5:5:5,5:0,0:0,0:6.65:0.00:0.00  26:26:0,0:24,24:2,2:25.5:0.00:0.00
chr16   24988884        .       C       CCA     .       PASS    IC=2;IHP=6;NT=ref;QSI=35;QSI_NT=35;RC=1;RU=CA;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1     DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   4:4:4,4:0,0:0,0:5.11:0.00:0.00  20:20:0,0:18,19:2,1:19.55:0.00:0.00
chr16   74566092        .       ATAT    A       .       PASS    IC=0;IHP=12;NT=ref;OVERLAP;QSI=32;QSI_NT=32;RC=1;RU=TAT;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1   DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   0:0:2,3:0,0:2,1:3.75:0.37:0.00  23:23:0,0:15,19:8,4:17.63:0.93:0.00
chr17   1933225 .       T       TG      .       PASS    IC=4;IHP=4;NT=ref;QSI=40;QSI_NT=40;RC=3;RU=G;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1      DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   8:8:7,8:0,0:1,0:8.34:0.26:0.00  16:16:0,0:16,16:0,0:17.01:0.00:0.00
chr17   41566783        .       CTCT    C       .       PASS    IC=1;IHP=6;NT=ref;QSI=41;QSI_NT=41;RC=2;RU=TCT;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1    DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   9:9:9,9:0,0:0,0:7.33:0.00:0.00  14:14:0,0:14,14:0,0:14.43:0.00:0.00
chr19   3192358 .       TGGGCTG T       .       PASS    IC=3;IHP=4;NT=ref;QSI=44;QSI_NT=44;RC=4;RU=GGGCTG;SGT=ref->hom;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   6:6:6,6:0,0:0,0:7.5:0.00:0.00   20:20:0,0:18,20:2,0:22.22:0.41:0.00
chr19   49519785        .       CT      C       .       PASS    IC=0;IHP=4;NT=ref;Q

Should I use TOR as the ALT for normal and as REF for the tumor? In some cases, for example the second indel in the vcf, the total DP is higher than TAR for normal samples (6 DP vs 7), why?

How can I obtain the count for REF and ALT of both tumor and normal sample pairs? If I get these counts I can calculate the allele frequencies.

Thank you in advance for your help!

Best