jvarkit

Biostar497922

Split VCF into separate VCFs by SNP count

Usage

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

Usage: java -jar dist/jvarkit.jar biostar497922  [options] Files

Usage: biostar497922 [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    -C, --chrom
      by chromosomes when using '-n'.
      Default: false
    --count, -n
      number of variants per vcf
      Default: -1
    -d, --distance
      max distance beween consecutive variants (ignore if <=0) . 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
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --index
      start numering file index from 'x'
      Default: 1
    -D, --length
      max distance beween first and last variant (ignore if <=0) . 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
    -m, --manifest
      output manifest to this file.
  * -o, --output
      Output directory
    --prefix
      file prefix
      Default: split
    --version
      print version and exit

Keywords

• vcf

See also in Biostars

• https://www.biostars.org/p/497922

Creation Date

20210319

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar497922.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 biostar497922 ? 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/biostar497922.jar -n 10 -o TMP src/test/resources/rotavirus_rf.vcf.gz
[INFO][Biostar497922]Writing TMP/split.000001.vcf.gz
[INFO][Biostar497922]Writing TMP/split.000002.vcf.gz
[INFO][Biostar497922]Writing TMP/split.000003.vcf.gz
[INFO][Biostar497922]Writing TMP/split.000004.vcf.gz
[INFO][Biostar497922]Writing TMP/split.000005.vcf.gz
[INFO][Biostar497922]. Completed. N=45. That took:0 second


t$ find TMP/ -type f -name "*.vcf.gz" | sort | while read F; do echo -n "$F " && gunzip -c $F | grep -v "#" | wc -l  ; done
TMP/split.000001.vcf.gz 10
TMP/split.000002.vcf.gz 10
TMP/split.000003.vcf.gz 10
TMP/split.000004.vcf.gz 10
TMP/split.000005.vcf.gz 5

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