jvarkit

SplitVcf

split a vcf using a named list of intervals…

DEPRECATED

use bcftools and a loop

Usage

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

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

Usage: splitvcf [options] Files
  Options:
    -g, --groupfile
      Chromosome group file. Intervals are 1-based. If undefined, splitvcf 
      will use the sequence dictionary to output one vcf per contig.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --multi
      if set, allow one variant to be mapped on multiple chromosome group (the 
      record is duplicated)
      Default: false
  * -o, --out
      Output filename. Name must contain '__GROUPID__'
    -u, --unmapped
      unmapped interval name
      Default: OTHER
    --version
      print version and exit

Keywords

• vcf

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SplitVcf.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/SplitVcfTest.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 splitvcf ? 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

Example

$ cat groups.txt

G1	10:112583204-112583210
G2	11
G3	12:1234-1235 13:20-30

$ java -jar dist/splitvcf.jar  -o tmp__GROUPID__.vcf.gz -g groups.txt in.vcf
$ ls tmp*
tmpG1.vcf.gz
tmpG2.vcf.gz
tmpG3.vcf.gz
tmpOTHER.vcf.gz

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