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genetics-statistics / faster_lmm_d

A faster lmm for GWAS. Supports GPU backend.
GNU General Public License v3.0
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VCF support #34

Open prasunanand opened 6 years ago

prasunanand commented 6 years ago

Add IO to read VCF files

pjotrp commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 :)