Mean Genotype File Format from PLINK PED (.bed+.bim+.fam) file set for gemma-wrapper · Biostar

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Mean Genotype File Format from PLINK PED (.bed+.bim+.fam) file set for gemma-wrapper

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...

plink bimbam qtl gemma

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written 4.1 years ago by abc •

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