VCFtools-Teaching: Difference between revisions
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The last version of this application is at /usr/local/apps/eb/VCFtools/0.1.15-foss-2016b-Perl-5.24.1 | 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 | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 | ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> | ||
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=VCFtools.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=VCFtools.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=VCFtools.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 | ml VCFtools/0.1.15-foss-2016b-Perl-5.24.1 | ||
vcftools --help | |||
VCFtools (0.1.15) | VCFtools (0.1.15) | ||
Latest revision as of 13:10, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
0.1.15
Author / Distributor
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
#SBATCH --error=VCFtools.%j.err
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 --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
Installation
Source code is obtained from VCFtools
System
64-bit Linux