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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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How should the alt alleles *,* be interpreted here #216

Closed sstadick closed 2 years ago

sstadick commented 2 years ago

Describe the bug

In the following selectino for chr13:34885776, how should the *,* be interpreted?

chr13   34884525        .       C       T       60.35   PASS    AC=1;AN=2;DP=25;MQ=60;NS=1;QD=2.414;RFGQ_ALL=8.54;STRL=2;STRP=1 GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      0|1:60:25:60:34884525:100:28,6:41,41:0.247:8.54:PASS
chr13   34884622        .       A       G       95.53   PASS    AC=1;AN=2;DP=23;MQ=60;NS=1;QD=4.153;RFGQ_ALL=11;STRL=5;STRP=2   GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      0|1:95:23:60:34884525:100:25,4:41,41:0.372:10.97:PASS
chr13   34885774        .       AAG     A       60.84   PASS    AC=2;AN=2;DP=25;MQ=57;NS=1;QD=2.434;RFGQ_ALL=6.12;STRL=21;STRP=10       GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      1|1:13:25:57:34885774:48:.,33:.,.:.:6.12:PASS
chr13   34885776        .       GAGAAAGAA       *,*     16.04   PASS    AC=1,1;AN=2;DP=26;MQ=57;NS=1;QD=0.617;RFGQ_ALL=6.02;STRL=62;STRP=4      GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      1|2:16:26:57:34885774:48:.,34,34:.,.,.:.:6.02:PASS
chr13   34885786        .       GAA     G       20.38   RF      AC=1;AN=2;DP=26;MQ=57;NS=1;QD=0.784;RFGQ_ALL=1.67;STRL=62;STRP=4        GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      1|0:20:26:57:34885774:48:35,1:41,.:0.49:1.67:RF
chr13   34885828        .       AAGAAAGAAAGAAAG A       8.64    PASS    AC=1;AN=2;DP=35;MQ=59;NS=1;QD=0.247;RFGQ_ALL=3.1;STRL=66;STRP=4 GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      1|0:8:35:59:34885828:100:36,14:41,.:0.266:3.1:PASS
chr13   34885891        .       G       GAAAGAGAAAAAAAGAAAGGAAAGA       209.27  PASS    AC=1;AN=2;DP=37;MQ=58;NS=1;QD=5.656;RFGQ_ALL=5.85;STRL=15;STRP=7        GT:GQ:DP:MQ:PS:PQ:AD:BQ:SB:RFGQ:FT      1|0:209:37:58:34885891:38:43,11:37,.:0.298:5.85:PASS

Version

$ octopus --version
octopus version 0.7.4 (HEAD ed012a6e)
Target: x86_64 Linux 5.4.0-1058-aws
SIMD extension: AVX512
Compiler: GNU 11.2.0
Boost: 1_76

Command

Command line to run octopus:

octopus 
--reference {input.ref}
--reads {input.bam}
--output {output.vcf}
--forest {input.forest} 
--threads {threads}
--max-reference-cache-memory 1G
--target-read-buffer-memory 8G 
--caller individual
--annotations AD SB BQ STRL STRP QD
sstadick commented 2 years ago

Closing as dup of https://github.com/luntergroup/octopus/issues/215