jvarkit

VcfLiftOver

Lift-over a VCF file

Usage

Usage: vcfliftover [options] Files
  Options:
    --adaptivematch
      Use adapative liftover minmatch using the ratio between the min allele 
      size and the longest allele size
      Default: false
  * -f, --chain
      LiftOver file.
    --chainvalid
      Ignore LiftOver chain validation
      Default: false
    -check, --check
      Check variant allele sequence is the same on REF
      Default: false
    -x, --failed
      (file.vcf) write variants failing the liftOver here. Optional.
    -failtag, --failtag
      failed INFO tag
      Default: LIFTOVER_FAILED
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --indel, --indels
      do not LiftOver indels
      Default: false
    --info
      remove attribute from INFO on the fly
      Default: []
    -m, --minmatch
      lift over min-match.
      Default: 0.95
    -o, --output
      Output file. Optional . Default: stdout
  * -D, -R, -r, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -T, --tag
      INFO tag
      Default: LIFTOVER
    --version
      print version and exit

Keywords

• vcf
• liftover

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfliftover

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/VcfLiftOver.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/liftover/VcfLiftOverTest.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 vcfliftover ? 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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