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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Can I disable the SB flag when not used? #75

Open Manuel-DominguezCBG opened 1 year ago

Manuel-DominguezCBG commented 1 year ago

In our test, we only obtained R1 reads. I was wondering if there is a way to not flag variants based on SB. Is this possible?

My code

apptainer exec --bind "$ref_folder":"$ref_folder" \
               "$pisces"  dotnet /app/Pisces_5.2.9.122/Pisces.dll \
               -bam  "${Sample_ID}"_FINAL_SORTED.bam \
               -g  "$piscesrefgenomefolder" \
               -o ./ \
               -i "$ampliconscoordenatesbed"  \
               --gvcf false \
               --minvq 20 \
               --maxvq 100 \
               --minbq 20 \
               --mindpfilter 5000 \
               --ssfilter False\
               --minmq 20 \
               --mindp 10

and a couple of variants


#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  2111700067_FINAL_SORTED.bam
chr5    171410472   .   G   C   80  LowDP;NC;SB DP=14   GT:GQ:AD:DP:VF:NL:SB    0/1:80:4,6:14:0.429:20:-100.0000
chr5    171410482   .   A   T   100 LowDP;NC;SB DP=969  GT:GQ:AD:DP:VF:NL:SB    0/1:100:919,49:969:0.051:20:-100.0000

I know that the tool is not filtering out variant based on SB but it is weird that the flag is still there.

tamsen commented 1 year ago

hi! can you re-post in https://github.com/tamsen/Pisces/, and I'll answer there. Thanks!