EIGENSOFT-Teaching: Difference between revisions
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=== Version === | === Version === | ||
7.2.1 | |||
===Author / Distributor=== | ===Author / Distributor=== | ||
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Also refer to [[Running Jobs on the teaching cluster]] | Also refer to [[Running Jobs on the teaching cluster]] | ||
*Version | *Version 7.2.1, installed in /apps/eb/EIGENSOFT/7.2.1-foss-2022a | ||
To use this version of EIGENSOFT, please first load the module with | To use this version of EIGENSOFT, please first load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
module load EIGENSOFT/7.2.1-foss-2022a | |||
module load EIGENSOFT/7.2.1-foss- | |||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml EIGENSOFT/7.2.1-foss- | ml EIGENSOFT/7.2.1-foss-2022a<br> | ||
smartpca [options]<br> | smartpca [options]<br> | ||
</div> | </div> | ||
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<pre class="gcomment"> | <pre class="gcomment"> | ||
module load EIGENSOFT/7.2.1-foss- | module load EIGENSOFT/7.2.1-foss-2022a | ||
smartpca | smartpca | ||
no parameters | no parameters | ||
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=== Installation === | === Installation === | ||
Version 7.2.1: Source code from https://github.com/DReichLab/EIG/archive/ | Version 7.2.1: Source code from https://github.com/DReichLab/EIG/archive/ | ||
Latest revision as of 13:37, 6 September 2023
Category
Bioinformatics
Program On
Teaching
Version
7.2.1
Author / Distributor
Description
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. More information: http://www.hsph.harvard.edu/alkes-price/software/
Running Program
Also refer to Running Jobs on the teaching cluster
- Version 7.2.1, installed in /apps/eb/EIGENSOFT/7.2.1-foss-2022a
To use this version of EIGENSOFT, please first load the module with
module load EIGENSOFT/7.2.1-foss-2022a
Sample job submission script (sub.sh) to run version 7.2.1:
#!/bin/bash
#SBATCH --job-name=eigenjob
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=4gb
#SBATCH --time=08:00:00
#SBATCH --output=eigenjob.%j.out
#SBATCH --error=eigenjob.%j.err
cd $SLURM_SUBMIT_DIR
ml EIGENSOFT/7.2.1-foss-2022a
smartpca [options]
where [options] need to be replaced by the options (command and arguments) you want to use.
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Sample job submission command:
sbatch sub.sh
Documentation
module load EIGENSOFT/7.2.1-foss-2022a smartpca no parameters ## smartpca version: 16000
Installation
Version 7.2.1: Source code from https://github.com/DReichLab/EIG/archive/
System
64-bit Linux