Nan Hu
Department of Biological Sciences
Texas Tech University
Folders:
- bam - reads mapping
- codes for mapping sequence capture reads to reference genome
- vcf - variants calling
- codes for calling SNPs from mapped population
- filter the vcf files with criteria screened from reads status distribution
- fst analysis mapping out the SDR region
- phase - phasing X and Y haplotype
- bash scripts in using BEAGLE 5.0 to phase haplotypes
- python scripts to extract haplotypes
- phylogeny reconstruction of X and Y haplotypes