split gtex genotype data by chromosomes.

Hello,

I used and edited the command line to use –vcf to import vcf file.

I used these commands:

for chr in $(seq 1 22); do

     plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz
           –chr $chr
           –recode
           –out /scratch/TWAS/data_download/new_rna-seq/myGwasData.chr$chr ;
done

 and then i used this command:

plink –ped myGwasData.chr1.ped –map myGwasData.chr1.map –recode vcf –out chr1_impute_qc

Its generating separate .ped and .map file for each chromosomes and then i got my vcf file for individual chromosomes using .ped and .map file 

I just wanted to take your advice whether this is correct step to do it? or should i do it in some other way.

I don’t have .bed file for GTEx vcf file.

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