vcftools

Owned by Indy Siva
Dec 10, 2015
1 min read

Introduction

http://vcftools.sourceforge.net/options.html
The vcftools program is intended for analysis of diploid SNP data in VCF format. The program is run from the command line, and the interface is inspired by PLINK, and so should be largely familiar to users of that package. Commands take the following form:

vcftools --vcf file1.vcf --chr 20 --freq

Usage

module load bioinformatics/vcftools/0.1.9

Installation

mkdir -p /sw/bioinformatics/vcftools/0.1.9/src
tar -zxvf vcftools_0.1.9.tar.gz
cd /sw/bioinformatics/vcftools/0.1.9/src/vcftools_0.1.9

#module load perl/5.12.4
module load perl/5.15.8
make

Reference

1. http://vcftools.sourceforge.net/options.html