Question: How to filter .vcf based on .gbk file to remove SNP calls in non-CDS regions?
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goatsrunfaster • 20 wrote:
I have a VCF file with multiple individuals mapped to a reference. What I would like to do is filter the VCF file so it only includes SNPs from CDS regions. I have a genbank (.gbk) from NCBI for the reference which includes CDS regions. Is there a simple way to do this? I can't seem to find any resources related to this type of filtering.
Additionally, once this filtering is complete I would like to filter synonymous SNPs from the vcf, so I am left with only non-synonymous SNPs in coding regions for my final VCF file.
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modified 13 months ago
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Pierre Lindenbaum ♦ 133k
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13 months ago by
goatsrunfaster • 20
