EIGENSOFT-Sapelo2 - Revision history

Shtsai at 00:33, 5 April 2026

2026-04-05T00:33:05Z

← Older revision		Revision as of 20:33, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]

	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	7.2.1		7.2.1

	===Author / Distributor===		==Author / Distributor==

	[https://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT]		[https://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT]

	===Description===		==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/		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 ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	=== Documentation ===		== Documentation ==

	<pre class="gcomment">		<pre class="gcomment">
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	</pre>		</pre>

	=== 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/

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea at 13:26, 16 July 2025

2025-07-16T13:26:57Z

← Older revision		Revision as of 09:26, 16 July 2025
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	*Version 7.2.1, installed in /apps/eb/EIGENSOFT/7.2.1-foss-~~2022a~~		*Version 7.2.1, installed in /apps/eb/EIGENSOFT/7.2.1-foss-2024a

	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-2024a
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml EIGENSOFT/7.2.1-foss-~~2022a~~<br>		ml EIGENSOFT/7.2.1-foss-2024a<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-~~2022a~~		module load EIGENSOFT/7.2.1-foss-2024a
	smartpca		smartpca
	no parameters		no parameters

Chelsea: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 7.2.1 ===Author / Distributor=== [https://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT] ===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 use..."

2024-05-14T16:15:42Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 7.2.1 ===Author / Distributor=== [https://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT] ===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 use..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]

=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

7.2.1

===Author / Distributor===

[https://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT]

===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 Sapelo2]]

*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
<pre class="gscript">
module load EIGENSOFT/7.2.1-foss-2022a
</pre>

Sample job submission script (sub.sh) to run version 7.2.1:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=eigenjob 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=4gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=eigenjob.%j.out 
<nowiki>#</nowiki>SBATCH --error=eigenjob.%j.err 

cd $SLURM_SUBMIT_DIR 
ml EIGENSOFT/7.2.1-foss-2022a 
smartpca [options] 
</div>
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:'''

<pre class="gcommand">
sbatch sub.sh
</pre>

=== Documentation ===

<pre class="gcomment">
module load EIGENSOFT/7.2.1-foss-2022a
smartpca
no parameters
## smartpca version: 16000
</pre>

=== Installation ===

Version 7.2.1: Source code from https://github.com/DReichLab/EIG/archive/

=== System ===
64-bit Linux