jvarkit

ConvertBedChromosomes

Last commit

Convert the names of the chromosomes in a Bed file

Usage

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

Compilation

Requirements / Dependencies

Download and Compile

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

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/misc/ConvertBedChromosomes.java

Contribute

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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