Detecting Polymorphic sites from VCF file
I generated a VCF file and my goal is to find top genes with most polymorphic sites. I understand what the format of the VCF file is and I have SNPs, Indels, variants with multiple alleles, etc. But I am not sure what tool I can use to extract variants with most polymorphic sites.
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jigarnt •
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mmukhame321 •
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mmukhame321 •
1 answer
It depends a lot on your organism. You can use VCFtools to filter out your variants or you can look at every site for 0% SNP reads in reference genome and 100 % SNP reads in your sample by looking it in the genome viewer like IGV and TABLET.
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