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How to convert scaffold name to chromosome number in vcf file

How to convert scaffold name to chromosome number in vcf file? for example

NC3251.1 convert to 1
NC3252.1 convert to 2

I would be very grateful if you could help me solve this problem.

vcf scaffold chromosome
• 1,668 views • link
written by kk.mahsa kk.mahsa

1 answer 

awk '{printf("%s\t%d\n",$1,NR);}' /path/to/ref.fasta.fai > change.txt

and then

bcftools annotate --rename-chrs  change.txt in.vcf
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you Pierre, it worked for me

• 0 views • link
written by kk.mahsa kk.mahsa

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