Detecting Polymorphic sites from VCF file

Question

[mmukhame321]

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.

Answer 1

[jigarnt]

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.

• http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it