jvarkit

AlmostSortedVcf

Last commit

Sort an ‘almost’ sorted VCF. Most variants should be sorted but a few consecutive lines might have been switched by a caller.

DEPRECATED

USE BCFTOOLS

Usage

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

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

Usage: almostsortedvcf [options] Files
  Options:
    -N, --buffersize
      max records in ram
      Default: 1000
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/sortvcfonref/AlmostSortedVcf.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 almostsortedvcf ? 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

Warning

Barey used. Just use bcftools sort…

Example

$  java -jar dist/almostsortedvcf.jar < in.vcf > out.vcf

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