VCF support

[prasunanand]

Add IO to read VCF files

[pjotrp]

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]

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]

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 :)