VcfSplitBed

Last commit

Split VCF by BED/Region Name

Usage

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

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

Usage: vcfsplitbed [options] Files
  Options:
  * -B, --bed
      User bed fourth column is used as the key to aggregate the variants. 
      Empty is replace with {chrom}_{start}_{end}
    --disable-hash-directory, --dhd
      disable default which is to save each file in a checksum-based 
      directory-a-la-nextflow to avoid a large number of files in the same 
      directory. 
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --prefix
      prefix each output VCF file with this string
      Default: <empty string>
    --version
      print version and exit

Keywords

  • vcf
  • sliding
  • window

Creation Date

20190619

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfsplitbed/VcfSplitBed.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfsplitbed ? 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

$ java -jar dist/jvarkit.jar vcfsplitbed --bed input.ned src/test/resources/rotavirus_rf.vcf.gz

see also

  • vcfgenesplitter