jvarkit

VcfSplitNVariants

Last commit

Split VCF to ‘N’ VCF files

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:
    -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
      number of variants. Or use --vcf-count
      Default: -1
    --vcf-count
      number of output vcf files. Or use --variants-count
      Default: -1
    --version
      print version and exit

Keywords

See also in Biostars

Creation Date

202221122

Source code

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

Contribute

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
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