How to add contigs name and length to the header of a VCF file ?

Question

[mohsamir2016]

Dear all,

I am trying hard to add contigs information to the header of a vcf file because when I try to modify the names of chromosomes in a VCF file using

bcftools annotate --rename-chrs Names.txt gallus_gallus.vcf -Ov -o gallus_gallusrenamed.vcf

It gave me the following error :

[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
Encountered an error, cannot proceed. Please check the error output above.
If feeling adventurous, use the --force option. (At your own risk!)

By checking the unique names of the contigs in this VCF file using

bcftools query -f '%CHROM\n' gallus_gallus.vcf|uniq

I realized that it gave me:

So I think I need to first add the contig tag to VCF header

Could any one suggest a code for that?

Thanks

Answer 1

[Pierre Lindenbaum]

UpdateVcfSequenceDictionary https://gatk.broadinstitute.org/hc/en-us/articles/360042477832-UpdateVcfSequenceDictionary-Picard-

or

bcftools reheader --fai https://samtools.github.io/bcftools/bcftools.html#reheader

[mohsamir2016]

Thanks, can you explain more, I think the first option is more convenient (i.e. UpdateVcfSequenceDictionary https://gatk.broadinstitute.org/hc/en-us/articles/360042477832-UpdateVcfSequenceDictionary-Picard-)

Does this means that my command might look like :

gatk UpdateVcfSequenceDictionary -I oldfile.vcf -O newfile.vcf -SD referencegenome.dict

In such case, the input is the old VCF, outputing the newfile, and then I used the dictionarized fasta file of the reference genome ?

Thanks