jvarkit

ConvertLiftOverChain

Last commit

Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc…)

Usage

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

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

Usage: convertliftoverchain [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -R1, --ref1
      Source chain REFference mapping. Default : no conversion. Chromosome 
      mapping file. If the file looks like a NGS file (fasta, vcf, bam...) the 
      mapping is extracted from a dictionary; Otherwise, it is interpreted as 
      a mapping file ( See https://github.com/dpryan79/ChromosomeMappings )
    -R2, --ref2
      Destination chain REFference mapping. Default : no conversion. Indexed 
      fasta Reference file. This file must be indexed with samtools faidx and 
      with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit

Keywords

Creation Date

20190409

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/liftover/ConvertLiftOverChainTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite convertliftoverchain ? 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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