Mean Genotype File Format from PLINK PED (.bed+.bim+.fam) file set for gemma-wrapper
Entering edit mode
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 ( file set with PLINK
3) recoded ( 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

Login before adding your answer.

Traffic: 796 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6