VcfCluster

Last commit

VCF

Usage

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

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

Usage: vcfcluster [options] Files
  Options:
    -f, --force
      force writing
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -L, --length, -n
      max-length per cluster. A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 1000000
    --no-group-bnd
      disable grouping variants with INFO/SVTYPE=BND  having same 
      ID=INFO/MATEID 
      Default: false
    --no-index
      do no write tbi index
      Default: false
  * -o, --output
      output directory
    -p, --prefix
      file prefix
      Default: split.
    -seed, --seed
      random see: -1= current-time. Random is used to add a variant to a 
      random available batch
      Default: -1
    --version
      print version and exit

Keywords

vcf
cluster
cnv
sv

Creation Date

20260108

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcluster/VcfCluster.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfcluster/VcfClusterTest.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 vcfcluster ? 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

Motivation

split CNV/SV vcf by clusters of size='x' for later parallelization (e.g: duphold, annotation, etc...) All INFO/SVTYPE=BND are grouped in the same cluster using ID and INFO/MATEID

Example

java -jar dist/jvarkit.jar vcfcluster -o TMP manta.vcf.gz