In Plink2, when converting a VCF file to bed format - how to retain original chromosome names?

Question

[rijan_dhakal2055]

When I convert a VCF to bed format using plink2 - is there a way I can retain the original Chromosome names as they were in the VCF file.

I am working with non-human data and if my chromosome names are Chr01 then Plink2 converts them to 1 and this is causing some downstream issues.

How can I just retain the old names as is?

Answer 1

[chrchang523]

You cannot retain the names as-is. (Plink2 pretty much has no choice but to standardize them; there is far too much pointless friction re: "1" vs. "chr1" without that.)

Instead, after exporting a VCF file, use the --rename-chrs flag with "bcftools annotate".

[rijan_dhakal2055]

Thank you for the confirmation!