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Feature request: input & output VCF #7

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bredeson opened this issue Dec 4, 2023 · 0 comments
Open

Feature request: input & output VCF #7

bredeson opened this issue Dec 4, 2023 · 0 comments

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@bredeson
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bredeson commented Dec 4, 2023

Dear AlphaGenes Devs,
I use AlphaFamImpute for imputing and phasing F1/outbred plant populations for genetic linkage mapping and QTL analysis, and I find it very accurate and useful for these purposes. I love this excellent tool!

I have a feature request: I would very much like to see (bgzip-compressed) VCF/BCF file support in AlphaFamImpute. The pysam module provides a fast VCF/BCF parsing API that can be used to facilitate reading/writing VCF/BCF files (viapysam.VariantFile()).

Thank you for providing this software!

  • Jessen
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@bredeson