APOE Genotype Coding

Introduction

This small piece of nifty script takes in a folder of VCF/ VCF.gz files and genotypes APOE. In the end, we have a single report file with the name of sample and the genotype.

Requirements

The script is written in shell script and requires only BCFTools to be installed on the system apart from some default tools such as awk/ sed/ grep etc. The script only supports Linux/ Unix/ macOS

Usage

Usage: apoec.sh <VCF_DIR> <TSV_DIR> <VCF_REGEX>
VCF_DIR: The directory where the VCF files are located.
TSV_DIR: The directory where the TSV files will be saved. Use the same directory as VCF_DIR if not specified.
VCF_REGEX: Get custom regex to filter VCF/VCF.gz files. Use all VCF/ VCF.gz files if not specified.

System Requirements

Unix/ Linux system with BASG/ ZSH
No specific package requirements, runs with basic UNIX tools in addition to:
* gunzip
* mawk/ awk: MAWK is recommended for speed gains!
These packages are almost always available by default or easily installable from the Linux package managers

Limitation

Currently only supports GRCh38, but, will add GRCh37 support later.