I have been running the Germline variant caller on some bam files and I am getting some strange allele calls. I seem to get a haploid allele call following every indel: See position 5140 into 5141 below for an example, but this seems to occur at every indel. Is this normal behaviour? I suppose that this is reflecting that position 5141 does not exist for the 2nd base pair of the allele without the insertion, but I don't understand why two alleles are specified (G & A at position 5141 in this example), and this formatting (only a single allele) is giving me errors in downstream analyses.
13 5139 . T . . PASS END=5141;BLOCKAVG_min30p3a;AN=0 GT:GQX:DP:DPF:MIN_DP ./.:.:.:.:.
13 5140 . TG T 95 PASS MQ=60;END=5151;BLOCKAVG_min30p3a;CIGAR=1M1D;RU=G;REFREP=2;IDREP=1;AC=1;AN=2 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL:DP:DPF:MIN_DP 0/1:103:27:17:8,8:6,4:2,4:PASS:137,0,100:.:.:.
13 5141 . G A 281 PASS SNVHPOL=3;MQ=60;AC=0;AN=1 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL:PS:MIN_DP 0:.:94:7:2:.:.:.:.:.:.:.:7
13 5142 . G . . PASS END=5227;BLOCKAVG_min30p3a;AN=2 GT:GQX:DP:DPF:MIN_DP 0/0:33:21:2:12
If this behaviour is expected, does Strelka have some simple way of filtering these sites out, or should I just do that separately? For reference, the commands I used to generate my variant calls are pasted below.
Hi!
I have been running the Germline variant caller on some bam files and I am getting some strange allele calls. I seem to get a haploid allele call following every indel: See position 5140 into 5141 below for an example, but this seems to occur at every indel. Is this normal behaviour? I suppose that this is reflecting that position 5141 does not exist for the 2nd base pair of the allele without the insertion, but I don't understand why two alleles are specified (G & A at position 5141 in this example), and this formatting (only a single allele) is giving me errors in downstream analyses.
If this behaviour is expected, does Strelka have some simple way of filtering these sites out, or should I just do that separately? For reference, the commands I used to generate my variant calls are pasted below.
Many thanks!!