Fixed differences

This R script was used to identify loci with SNPs that are differently fixed between males and females (ie all males are heterozygous, all females are homozygous). The loci identified are on the sex chromosomes, but given our parameters they have not diverged enough for Stacks to split them into separate loci. We tested the scrip on loci that mapped to select scaffolds where sex-specific markers were found, and then we applied the script to filter the entire sumstats.tsv file.