Find sex specific loci from genome-wide genetic markers

Note: only accept SNPs.

Usage

    -i: input GT file.
    -o: output file.
    -p: popmap file.
    -c: coverage.
    -e: error rate. 
    -h: help message.

Examples

1. GT file can be generated by VCFtools.

   vcftools --vcf input.vcf --extract-FORMAT-info GT

2. popmap file, a tab separated file including individuals' name and their corresponding sex type ('female' or 'male'). e.g.

   ind1 female

   ind2 female

   ind3 male

   ind4 male

3. coverage should be adjusted according to your data.

4. error rate should be set to 0 if you just want exclusive loci.

5. an example run, 12 individuals are required to be exclusively sex specific in one sex:

   find_sex_loci_from_GT.pl -i GT.sample -p popmap -o output -c 12 -e 0
   

   output

Contact Yulong Li