jvarkit

BigwigMerge

merge several Bigwig files using different descriptive statistics (mean, median, etc..)

Usage

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

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

Usage: bigwigmerge [options] Files
  Options:
    --header
      write track header
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --interval, -r
       process only this interval
    --method, -m
       how to compute merge of wiggle values ?
      Default: median
      Possible Values: [median, average, count, sum, min, max, random]
    --min-item-count
       skip output data if thre is less than 'x' bigwig file at a location
      Default: 0
    --min-value
       skip output data with values lower than 'x'
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
    --version
      print version and exit

Keywords

• wig
• bigwig

Creation Date

20240417

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.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 bigwigmerge ? 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

motivation

merge several Bigwig files using different descriptive statistics (mean, median, etc..)

Output is a BedGraph file.

Input is a set of bigwig file or a file with the ‘.list’ suffix containing the path to the bigwig

Example

find DIR -type f -name "*.bigWig" > tmp.list
java -jar jvarkit.jar bigwigmerge -R genome.fa tmp.list --interval "chr1:234-567" --header --method median  > bedGraph.bed

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