jvarkit

VcfFilterByLiftOver

Add FILTER(s) to a variant when it is known to map elsewhere after liftover.

Usage

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

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

Usage: vcffilterbyliftover [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
  * -f, --chain
      LiftOver file.
    --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].
    --lifted-filtered-vcf
      Another VCF in the destination reference. Input VCF will be filtered if 
      this vcf is FILTERed at the same lifted position.
    -m, --minmatch
      lift over min-match.
      Default: 1.0
    --no-validation
      Disable dictionary validation
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -D
      final distance. We look for weird distance between the current and the 
      previous variant on the same contig.Two variants initially distance < d 
      should have a distance <D after lift over.
      Default: 1500
    -d
      initial distance. See option -D.
      Default: 1000

Keywords

• vcf
• liftover

Creation Date

20190418

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/VcfFilterByLiftOver.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 vcffilterbyliftover ? 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

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