VcfSplitNVariants

Split VCF to 'N' VCF files, or by number fo variant of by distance between variants

Usage

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

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

Usage: vcfsplitnvariants [options] Files
  Options:
    --distance
      distance between variants. Or use --variants-count or --vcf-count. A 
      distance specified as a positive integer.Commas are removed. The 
      following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: -1
    -f, --force
      overwrite existing files
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --tbi, --index
      index on the fly as tbi files
      Default: false
    -m, --manifest
      write optional manifest to that file.
  * -o, --output, --prefix
      files prefix
    --variants-count, --vc-count, --n-variants
      number of variants. Or use --vcf-count or --distance
      Default: -1
    --vcf-count, --n-vcfs
      number of output vcf files. Or use --variants-count or --distance
      Default: -1
    --version
      print version and exit

Keywords

• vcf

See also in Biostars

• https://www.biostars.org/p/9548193

Creation Date

20221122

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfsplit/VcfSplitNVariants.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfsplit/VcfSplitNVariantsTest.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 vcfsplitnvariants ? 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 VCF to 'N' VCF files

example

$ java -jar dist/vcfsplitnvariants.jar --vcf-count 10 src/test/resources/rotavirus_rf.vcf.gz -o SPLITVCF --manifest jeter.mf --index -R src/test/resources/rotavirus_rf.fa
[INFO][VcfSplitNVariants]open SPLITVCF.00001.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00002.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00003.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00004.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00005.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00006.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00007.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00008.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00009.vcf.gz
[INFO][VcfSplitNVariants]open SPLITVCF.00010.vcf.gz

$ cat jeter.mf
vcf count   contigs
/home/lindenb/src/jvarkit-git/SPLITVCF.00001.vcf.gz 5   RF01,RF03,RF04,RF06,RF09
/home/lindenb/src/jvarkit-git/SPLITVCF.00002.vcf.gz 5   RF02,RF03,RF05,RF06,RF10
/home/lindenb/src/jvarkit-git/SPLITVCF.00003.vcf.gz 5   RF02,RF03,RF05,RF07,RF10
/home/lindenb/src/jvarkit-git/SPLITVCF.00004.vcf.gz 5   RF02,RF03,RF05,RF07,RF10
/home/lindenb/src/jvarkit-git/SPLITVCF.00005.vcf.gz 5   RF02,RF04,RF05,RF07,RF11
/home/lindenb/src/jvarkit-git/SPLITVCF.00006.vcf.gz 4   RF02,RF04,RF05,RF07
/home/lindenb/src/jvarkit-git/SPLITVCF.00007.vcf.gz 4   RF03,RF04,RF05,RF08
/home/lindenb/src/jvarkit-git/SPLITVCF.00008.vcf.gz 4   RF03,RF04,RF06,RF08
/home/lindenb/src/jvarkit-git/SPLITVCF.00009.vcf.gz 4   RF03,RF04,RF06,RF09
/home/lindenb/src/jvarkit-git/SPLITVCF.00010.vcf.gz 4   RF03,RF04,RF06,RF09