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VCF support #34

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prasunanand opened this issue May 1, 2018 · 3 comments
Open

VCF support #34

prasunanand opened this issue May 1, 2018 · 3 comments
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@prasunanand
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enhancement Feature

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@prasunanand
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Add IO to read VCF files
@prasunanand prasunanand self-assigned this May 1, 2018
@pjotrp
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pjotrp commented May 6, 2018

I would use bioruby-vcf to parse and filter VCF because it has great flexibility and it is ready for the future. If bio-vcf can output BIMBAM then there is no reason to add VCF support to GEMMA.

@prasunanand
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I agree. I will work on reading vcf files with help of bioruby-vcf . If everything goes fine, we won't need this feature in Faster_LMM_D :) .

@prasunanand
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qctool is easy to convert VCF to BIMBAM for VCF4.2. PLINK has some issue parsing VCFs due to allele size.

Discovered a bug in qctool.

https://bitbucket.org/gavinband/qctool/issues/48/converting-vcf-to-bimbam

Trying to use bioruby-vcf now :)

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