ConvertBedChromosomes

Convert the names of the chromosomes in a Bed file

Usage

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

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

Usage: bedrenamechr [options] Files
  Options:
    -c, --column
      1-based chromosome column(s), multiple separated by commas
      Default: 1
    -convert, --convert
      What should I do when  a converstion is not found
      Default: RAISE_EXCEPTION
      Possible Values: [RAISE_EXCEPTION, SKIP, RETURN_ORIGINAL]
    -d, --delim
      field delimiter.
      Default:  
    -s, --header
      Ignore lines starting with this java regular expression
      Default: (#|browser|track)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -f, --mapping, -m, -R
      load a custom name mapping.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 )
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• bed
• chromosome
• contig
• convert

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/ConvertBedChromosomes.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 bedrenamechr ? 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

$   curl -s http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz |\
    gunzip -c | \
    java -jar dist/bedrenamechr.jar -f src/main/resources/chromnames/hg19_to_g1kv37.tsv -c 2 |\
   tail


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uc004fxl.3  Y   +   59213948    59276439    59222135    59274621    7   59213948,59222126,59230781,59233166,59252482,59272370,59274552, 59214117,59222216,59230919,59233257,59252550,59272463,59276439, P51809-3    uc004fxl.3
uc004fxk.3  Y   +   59213948    59276439    59222135    59274809    7   59213948,59222126,59228291,59230781,59233166,59272370,59274552, 59214117,59222281,59228349,59230919,59233257,59272463,59276439, P51809-2    uc004fxk.3
uc011ncb.2  Y   +   59213948    59276439    59222274    59274621    7   59213948,59222126,59230781,59233166,59252482,59272370,59274552, 59214117,59222277,59230919,59233257,59252550,59272463,59276439, B4DE96  uc011ncb.2
uc010nxr.2  Y   +   59330251    59340490    59335611    59340461    9   59330251,59334000,59335576,59336119,59336347,59337090,59337948,59338753,59340193,   59330458,59334179,59335690,59336231,59336526,59337236,59338150,59338859,59340490,   B4E011  uc010nxr.2
uc004fxm.1  Y   +   59330251    59343488    59330414    59342523    9   59330251,59334078,59335552,59336119,59336354,59337119,59337948,59338753,59342486,   59330458,59334179,59335690,59336231,59336526,59337236,59338150,59338859,59343488,   B9ZVT0  uc004fxm.1
uc004fxn.1  Y   +   59330251    59343488    59330430    59343080    9   59330251,59335576,59336119,59336347,59337090,59337948,59338753,59340193,59342486,   59330458,59335690,59336231,59336526,59337236,59338150,59338859,59340278,59343488,   Q01113  uc004fxn.1
uc004fxo.1  Y   +   59352972    59356131    59353631    59356130    7   59352972,59354351,59354669,59354993,59355369,59355682,59355972, 59353819,59354463,59354816,59355130,59355505,59355884,59356131, I3L0A4  uc004fxo.1
uc022cpg.1  Y   +   59354984    59358336    59355427    59358045    7   59354984,59355369,59355682,59355972,59356790,59357702,59357911, 59355130,59355505,59355884,59356131,59356943,59357771,59358336, Q9NQA3  uc022cpg.1
uc011ncc.1  Y   -   59358328    59360854    59358328    59358328    3   59358328,59360006,59360500, 59359508,59360115,59360854, uc011ncc.1