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.
Read more here: Source link