This compressed directory contains three perl scrips used for filtering and processing the genetic data (i.e., the vcf file). morefilter_filtered2x-70_varsLycGwa.vcf was generated by running the two filter scripts. Most filters described in the paper are impelemented in the main script, vcfFilter.pl, which was run first. The second script, filterSomeMore.pl applies maximum coverage filters and a filter to drop variants that are near each other (within 3 bp in this case). The final scrips, vcf2gl.pl, extracts the genotype likelihoods from the vcf file
