Mean Genotype File Format from PLINK PED (.bed+.bim+.fam) file set for gemma-wrapper
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10 days ago
abc • 0

Hi folks,

from newbie:
gemma-wrapper requires BIMBAM file format with Mean Genotype File Format file.
I believe that PLINK1.9 with "--recode bimbam" flag outputs Basic Genotype File Format.
As I have PLINK PED (.bed+.bim+.fam) file set I tried:
1) recoded PLINK PED (.bed+.bim+.fam) file set to .vcf with PLINK
2) recoded .vcf to (.ped+.map) file set with PLINK
3) recoded (.ped+.map) file set to (geno+pheno+pos) BIMBAM file set with BIMBAM:
bimbam -g -p -pos -e -s -c --nobf -o -wmg

very doubt whether it's correct...

Any thoughts are welcome.

gemma plink qtl gemma-wrapper bimbam • 139 views
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