looking for variants only in autosomal chromosomes
 

Hello!

I'm trying to look for SNPs and indels in a wildcat genome sequenced by our lab, but the problem is that every reference genomes have been sequenced from female specimens and our genome has been sequenced from a male specimen, so we want to discriminate the sexual X and Y chromosomes and just search only for the variants present on autosomal chromosomes; so, my question is how to separate autosomal chromosomes from sexual chromosomes? Should I modify the BAM file obtained from the alignment between the reference genome and our sequenced genome, or should I modify the VCF file generated with BCFtools? And how?

Thank you for your replies.