SetFileFromBed

Last commit

Convert bed chrom/start/end/name sorted on 4th column to set file

Usage

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

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

Usage: setfilefrombed [options] Files
  Options:
    --disable-interval-merge
      Do not merge overlapping intervals in a setFile record
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout. For action=cluster, output is: 
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -t, --trim-chr
      Remove chr prefix in chromosome names on output.
      Default: false
    --version
      print version and exit

Keywords

setfile
bed

Creation Date

20210125

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/setfile/SetFileFromBed.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 setfilefrombed ? 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

$ echo -e "RF01\t150\t200\tA\nRF01\t190\t300\tA\nRF01\t350\t400\tA\nRF01\t150\t200\tB" |\
    java -jar dist/jvarkit.jar setfilefrombed -R src/test/resources/rotavirus_rf.fa frombed

A   RF01:151-300,RF01:351-400
B   RF01:151-200