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AntonioParra 09-13-2020 11:44 PM

looking for variants only in autosomal chromosomes

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.

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