error bcftools isec

Question

[lait]

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 ?

Answer 1

[jared.andrews07]

Sounds like you have trailing spaces/tabs in your header line. Or it requires actual sample calls. Check the spaces and remove them if present. If not, I'd probably just use bedtools intersect, as it can handle VCFs as well.

[lait]

yes, no spaces are present, I will try bedtools then, thanks for your answer.