How to convert a VCF to GATK VCF Format

Follow

Saeed Farajzadeh Valilou

• March 07, 2024 17:59

I have downloaded dbsnp v.156 vcf file from dbsnp ftp link and I want to convert it to GATK VCF format. And also I want to change chromosome notations (i.e. 'NC_000001.11' to 'chr1'). How can I do this?

0

• 

  Gökalp Çelik

  • March 07, 2024 18:05
  • Edited

  Hi Saeed Farajzadeh Valilou

  GATK does not have a specific VCF format however if you wish to convert contig names one of the best ways to do it is to use

  bcftools annotate --rename-chrs chrname.txt

  You may check how to use this tool via the manual in the link below.

  https://samtools.github.io/bcftools/bcftools.html#annotate 

  I hope this helps. 

  0

  Comment actions Permalink

Please sign in to leave a comment.