jvarkit

SwingPLinkSelectCluster

Swing-based Plink/MDS sample selector

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar swingplinkselectcluster  [options] Files

Usage: swingplinkselectcluster [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --samples-to-groups, -m
      a tab delimited file with two columns: (sample-name)(TAB)(group-name)
    --version
      print version and exit

Keywords

• plink
• sample
• swing

See also in Biostars

• https://www.biostars.org/p/9594882

Creation Date

20231123

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/plink/SwingPLinkSelectCluster.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite swingplinkselectcluster ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

GUI selecting the samples of a MDS file generated with plink. At the end a file with fid/iid/keep-status is saved.

Screenshot

see https://genomic.social/@yokofakun/112570150370091891

Input

input can be generated with plink:

Example:

	plink --bcf '${genome_bcf}' \\
		--double-id \\
		--read-genome '${genome_plink}' \\
		--mds-plot ${num_components} \\
		--cluster \\
		--out TMP/cluster

input file must have this header:

FID	IID	SOL	C1	C2	C3

Usage

java -jar dist/jvarkit.jar swingplinkselectcluster file.mds  --samples-to-groups sample2group.tsv

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