Sample ID conversion
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14 days 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.

Sample tools Bcf ID • 139 views
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