This repository comprises code and analyses for the targeted-sequencing of 1,845 rhesus macaques

Runing the analysis code only requires a standard computer with sufficient RAM to support in-memory operations.

The analysis is supported for Linux. The package has been tested on the following systems: Linux x86_64

R 4.0.0

python3.8

jdk1.8.0_121

GATK 4.0.0.0

PLINK v1.90b5.2

liftOver from UCSC genome browser

bcftools 1.17

macse_v0.9b1.jar

paml4.9j

ensembl-vep v.101

ANNOVAR v. 07/17/2017

dbNSFP v.3.5a

HGMD (v.12-20-2016)

ClinVar (v20230710)

The gnomAD database (v2.1.1)

caret_6.0-93 R package

cvAUC_1.1.4 R package

git clone https://github.com/fe4960/rhemac_retcap.git

See README.md in each sub folder

The test dataset, a vcf file, is in "test_data" folder.