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”.