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Removing "chr" from CHROM field

sp580sp580 GermanyMember


I intend to use a training resource VCF that contains "chr" in the CHR field (Reference obtained from UCSC), which is incompatible with my raw call set (reference obtained from ensembl).

I check the resource VCF and it only contains sites in autosomes, X, Y and MT, so there shouldn't be a problem with unplaced scaffolds nomenclature.

I was thinking about writing an expression that removes "chr", but I guess there is a better tool for the job that also takes care of the integrity of the VCF. However, I could not find any.

Could you please suggest what would be the best approach to solve this issue?

Thanks in advance!


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