Fst

Fst is an index of allelic fixation in populations, and so, if there are high levels of Fst within discrete genomic regions when comparing males to females, this would suggest that those regions differ between males and females and, therefore, are not recombining. For the SexFindR workflow, Fst is calculated from a biallelic vcf file using vcftools.

Example command

vcftools --gzvcf biallelic_filtered_PASS_fugu_14M_13F.vcf.gz --weir-fst-pop snpDen_males.txt --weir-fst-pop snpDen_females.txt --out biallelic_fst

Here, we make use of the same snpDen_males.txt and snpDen_females.txt reference files from the SNP Density step to assign individuals to their correct “population”.