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freebayes multi-allelic variants dissapear #33

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ViktorHy opened this issue Oct 20, 2023 · 1 comment

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ViktorHy commented Oct 20, 2023

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

Contributor Author

ViktorHy commented Oct 20, 2023 •

edited

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

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