Genome-wide allele frequency studies in Pacific oyster families identify candidate genes for tolerance to ostreid herpesvirus 1 (OsHV-1)

This repository contains the code used in a paper in the journal BMC Genomics.

Repository overview:

• SNP_pipeline.sh - Code to call and impute phased SNPs from genotyping-by-sequencing (GBS) data of biparental families
• AlphaFamImpute_prep.R - Code to generate the input files for the AlphaFamImpute program
• GWAFS.R - Code to run genome-wide allele frequency studies (GWAFS)