Entering edit mode
19 months ago
Madhusmita
•
0
I have used this command to convert .bgen file to vcf format for my imputed chromosome genotype data
bgenix -g ukb_imp_chr${CHR}_v3.bgen \
-i ukb_imp_chr${CHR}_v3.bgen.bgi \
-vcf -incl-rsids ${RSID} | \
bcftools reheader \
-h bgen_to_vcf/new_header.txt | \
I have a sample file which contains the IDs and gender information. the file has .sample extension a .txt file has 4 columns ID1 ID2 MISSING SEX. How do assign the IDs present in this file to my above vcf genotype file using above bcf tools reheader command.
Command as posted appears to be incomplete.