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Clinical-Genomics-Lund / SomaticPanelPipeline

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freebayes multi-allelic variants dissapear #33

Open ViktorHy opened 9 months ago

ViktorHy commented 9 months ago

When freebayes is merged with tnscope in aggregate_vcf.pl multiallelic sites just dissapear and only the tnscope call is left for one of the alleles.

I suspect it has to do with one of the multibreak alleles get GT 0/. in freebayes

ViktorHy commented 9 months ago

see /data/bnf/dev/viktor/myeloid/issues/issue_33 for information of a sample with this issue