BedMergeCnv

Merge continuous sorted bed records if they overlap a fraction of their lengths.

Usage

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

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

Usage: bedmergecnv [options] Files
  Options:
    -f, --fraction, --overlap
      Intervals will be merged if they both overlap this fraction of their 
      lengths. A decimal number between 0.0 and 1.0. If the value ends with 
      '%' it is interpretted as a percentage eg. '1%' => '0.01'. A slash '/' 
      is interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.9
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• bed
• chromosome
• contig

Creation Date

20200330

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bedtools/BedMergeCnv.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 bedmergecnv ? 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

input is bed on standard input or it's a set of interval files (.bed, .interval_list, .gtf, etc... )

output is a BED file:

• 4th column: number of items merged
• 5th column: fraction overlap with previous record
• 6th column an optional label. Concatenation of the distinct label. For a bed record the label is the 4th column. For a VCF record, the label is the name of the samples

Example

$ java -jar dist/bedmergecnv.jar src/test/resources/manta.B00*.vcf.gz | more

chr21   9653162 9653235 1   0.0
chr21   9653169 9653243 1   0.89
chr21   9653357 9653502 1   0.00
chr21   9660834 9660835 3   0.00
chr21   9841718 9842058 2   0.00
chr21   9846433 9846531 1   0.00
chr21   9846456 9846557 1   0.74
chr21   9846481 9846580 1   0.75
chr21   9851247 9854008 1   0.00
chr21   9862002 9862003 1   0.00
chr21   9881949 9882060 1   0.00
chr21   9936419 9936560 1   0.00
chr21   10459126    10459235    3   0.00
chr21   10475193    10475513    1   0.00
chr21   10492877    10493042    3   0.00
chr21   10493815    10493874    1   0.00
chr21   10618665    10618720    1   0.00
chr21   10633657    10633709    1   0.00
chr21   10699831    10700200    2   0.00
(...)