jvarkit

BedLiftOver

LiftOver a BED file

Usage

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

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

Usage: bedliftover [options] Files
  Options:
  * -f, --chain
      LiftOver chain file. Can be a local chain file, a URL 'https://hgdownload.soe.ucsc.edu/goldenpath/hg19/liftOver/hg19ToCriGri1.over.chain.gz', 
      or a chain identifier like 'hg19ToHg38'.
    -c, --columns
      column indexes for chrom,start,end. Multiple chrom/start/end can be set 
      by groups of 3 intergers: e.g '1,2,3,6,7,8,10,11,12'
      Default: 1,2,3
    --chainvalid, --disable-chain-validation
      Ignore LiftOver chain validation
      Default: false
    -x, --failed
        write bed failing the liftOver here. Optional.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --minmatch
      lift over min-match.
      Default: 0.95
    --original, --src
      Append original interval as CHROM:START-END
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
  * -D, -R2, -R, -r, --reference
      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
    -1
      coordinates are one-based (input is NOT bed)
      Default: false
    -R1
      Source of chromosome names to convert chromosome names ('chr1'->'1') for 
      the source assembly. Could be a dict, a fai, etc...

Keywords

• bed
• liftover

Creation Date

20140311

Source code

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

Unit Tests

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

cat in.bed | java -jar jvarkit.jar bedliftover --chain x.chain -R ref.fa

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