search

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
Other
633 stars 241 forks source link

Undefined header [W::vcf_parse] INFO 'PR' is not defined in the header, assuming Type=String #2198

Closed aainaGit closed 1 month ago

aainaGit commented 1 month ago

I am trying to rename chromosomes in a vcf file I received from Dartseq but I keep getting the below error. How do I fix this

unix command line code- bcftools annotate --rename-chrs chromosomes.txt bimbo312.vcf.gz -Oz -o renamebimbo312.vcf.gz

Error- [W::vcf_parse] INFO 'PR' is not defined in the header, assuming Type=String

When i zcat the vcf file, I see the following PR;DP=0 GT:AD:DP:GQ:PL

pd3 commented 1 month ago

You need to update the VCF header, please see the question answered here http://samtools.github.io/bcftools/howtos/FAQ.html#undefined-tag