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Short bash script that calculates pooled heterozygosity for 1 mb windows with .5 megabase overlaps

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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
#==============================================================================#

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Short bash script that calculates pooled heterozygosity for 1 mb windows with .5 megabase overlaps

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