Plink to bimbam format for gemma-wrapper

Question

[kumar.vinod81]

Hi, I want to use gemma-wrapper tool which needs files in BIMBAM format. Plink can convert from plink to BIMBAM format but it is very different from the real BIMBAM mean genotype format. Alleles come in two columns while BIMBAM needs them in mean genotype format. Is there any suggestion to convert plink or VCF file beautifully into BIMBAM format with mean genotype. Thanks,

Vinod,

Answer 1

[abc]

Hi, I also wanted to use gemma-wrapper...
Is it 100% that gemma-wrapper can't read PLINK binary PED file format (fam, .bim, .bed) ?
There is a thread on .vcf > BIMBAM conversion here:
https://github.com/genetics-statistics/GEMMA/issues/103