I am currently evaluating strelka2 for my PhD project and was very happy with the general output, but just now came to the case, where I know from ddPCR of that position, that there are actually 2 different snps at the same location for that one sample.
However strelka seems to only call the "more prevalent one" even though they appear at almost the same read count.
Is that something I can configure so it displays both these variants?
I have the relevant line of the vcf here
10 43615014 . G C . PASS SOMATIC;QSS=56;TQSS=1;NT=ref;QSS_NT=56;TQSS_NT=1;SGT=GG->CG;DP=325;MQ=60;MQ0=0;ReadPosRankSum=1.43;SNVSB=0;SomaticEVS=18.79 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 102:0:0:0:2,2:0,0:100,100:0,0 221:0:0:0:2,2:19,19:183,185:17,17
as you can see there are 19 and 17 reads respectively for each of the variants.
I am running strelka 2.9.2 if that is relevant to the question
Hey,
I am currently evaluating strelka2 for my PhD project and was very happy with the general output, but just now came to the case, where I know from ddPCR of that position, that there are actually 2 different snps at the same location for that one sample. However strelka seems to only call the "more prevalent one" even though they appear at almost the same read count. Is that something I can configure so it displays both these variants? I have the relevant line of the vcf here
10 43615014 . G C . PASS SOMATIC;QSS=56;TQSS=1;NT=ref;QSS_NT=56;TQSS_NT=1;SGT=GG->CG;DP=325;MQ=60;MQ0=0;ReadPosRankSum=1.43;SNVSB=0;SomaticEVS=18.79 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 102:0:0:0:2,2:0,0:100,100:0,0 221:0:0:0:2,2:19,19:183,185:17,17
as you can see there are 19 and 17 reads respectively for each of the variants.
I am running strelka 2.9.2 if that is relevant to the question
Thank you for your help and for an awesome tool