VcfTbiToBed

extracts BED for each contig in a tabix-indexed VCF peeking first of last variant for each chromosome.

Usage

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

Usage: java -jar dist/jvarkit.jar vcftbi2bed  [options] Files

Usage: vcftbi2bed [options] Files
  Options:
    --POS, -POS
      for the end position, default is to use the END position (think about 
      SV, INDEL...) of the variant. This option just use the POS.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• bed
• vcf
• tabix

Creation Date

20230214

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/tbi2bed/VcfTbiToBed.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 vcftbi2bed ? 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

Extract the first and last variants of a tabix-index-VCF file for each chromosome. Output is a BED file contig/start/end/vcf. Input can be:

• stdin (the path to the vcfs, one per line)
• the vcfs
• a file with the suffix '.list' containing the path to the vcfs, one per line.

Example: