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Symbolic alleles returned when --types ref requested #1757

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pd3 opened this issue Jul 20, 2022 · 0 comments
Open

Symbolic alleles returned when --types ref requested #1757

pd3 opened this issue Jul 20, 2022 · 0 comments

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@pd3
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pd3 commented Jul 20, 2022

Because the unseen star allele is not supported by bcf_get_variant_types, the command bcftools view --types ref is unable to distinguish between the star allele and other symbolic alleles, such as , , etc. This could be fixed either in bcftools or in bcftools+extend htslib API.

See samtools/htslib#1467 (comment) and samtools/htslib#1467 (comment)
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