Learning the Variant Call Format

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Evolutionary Bioinformatics Toolkit (EBT)

VCF: Variant Call Format files are difficult to understand at first, I already had to dive into them in order to learn how to edit them, so you can use my scripts. Some of these functions already exist in vcftools, but it seems it stopped being updated. so you can use these scripts to do various tasks with them

Checks vcf files and removes loci and samples with too many missings, can also input genotypes in missing (various options for this).