How to convert scaffold name to chromosome number in vcf file

Question

[kk.mahsa]

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.

Answer 1

[Pierre Lindenbaum]

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

[kk.mahsa]

Thank you Pierre, it worked for me