Pooled_Heterozygosity
ISU - Animal Breeding and Genetics Group
Author: Josue Chinchilla-Vargas
Created (date): 11/3/2020
Version (of the script): 1.0
Program (if applicable): Plink
Program Version (if applicable): 1.9
#==============================================================================#
Description
Calculates pooled heterozygosity (Hp) for 1 Mb windows
#==============================================================================#
Setup
Input files
.frq.counts (from Plink1.9 --freq counts)
Format: CHR SNP A1 A2 C1 C2 G0
.map used to calculate allele counts
Format: CHR SNP DISTANCE BP
Script works as follows:
./Hp.sh myfile.frq.counts myfile.map
Output files
Hp.txt
Format: CHR POS CHR_POS COUNT_MIN COUNT_MAJ NUM NUM Hp
#==============================================================================#