VCFtools-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.1.15

Author / Distributor

VCFtools

Description

"The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files." More details are at VCFtools

Running Program

The last version of this application is at /usr/local/apps/eb/VCFtools/0.1.15-foss-2016b-Perl-5.24.1

To use this version, please load the module with

ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_VCFtools
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=VCFtools.%j.out

cd $SLURM_SUBMIT_DIR
ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1
vcftools [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 
vcftools vcftools --help

VCFtools (0.1.15)
© Adam Auton and Anthony Marcketta 2009

Process Variant Call Format files

For a list of options, please go to:
	https://vcftools.github.io/man_latest.html

Alternatively, a man page is available, type:
	man vcftools

Questions, comments, and suggestions should be emailed to:
	vcftools-help@lists.sourceforge.net

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Installation

Source code is obtained from VCFtools

System

64-bit Linux