Removing "chr" from CHROM field
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!