I was trying this way here to find the intersection between two vcf files.
- Vcf file 1: a small vcf file containing some mutations that I am interested in.
- Vcf file 2: vcf file for chromosome X from gnomad database, so basically it contains a lot of useful allele frequencies annotations that I want to extract for my mutations in vcf file 1.
vcf file 2 (gnomad chrX) contains no sample names, just the following infotmation:
CHROM POS ID REF ALT QUAL FILTER INFO
When I run the bcftools command I get the following error:
gnomad.exomes.r2.1.1.sites.X.vcf.bgz [E::bcf_hdr_add_sample] Empty sample name: trailing spaces/tabs in the header line? Abgebrochen
any idea why ?