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All chromosomes and maq Layla Bioinformatics 1 02-13-2009 08:36 AM

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Old 09-13-2020, 10:44 PM   #1
AntonioParra
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Location: Seville, Spain

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Smile 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.
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bcf tools, indel analysis, snp analysis, variant detection, vcf filtering

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