[E::bcf_translate] Unchecked error (2) at chr10:10331, exiting

[hanguojun007]

Hi，when I concatenate some vcf file，it report this error. I don't understand the at chr10:10331 . What does that mean?

[hanguojun007]

Oh，this is the code: bcftools concat -a *.gz -D -Oz -o all.vcf.gz.

[pd3]

This is a generic error propagated from inside htslib and occurs when the program attempts to write a VCF/BCF line with unresolved tags.

In plain English: the input VCF most likely contains tags that are not defined in the header. I think that's probably causing the problem. To verify, you can run

bcftools view input.vcf.gz -o /dev/null

and check for messages such as

[W::vcf_parse_info] INFO 'X' is not defined in the header, assuming Type=String

Then you can use bcftools reheader to fix the problem by adding all missing tags.