jvarkit

MantaMerger

Merge Vcf from Manta VCF.

Usage

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

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

Usage: mantamerger [options] Files
  Options:
    --bnd-distance
      Two BND variants are the same if their bounds are distant by less than 
      xxx bases. A distance specified as a positive integer.Commas are 
      removed. The following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 100
    --check-bnd-mate
      When comparing two BND, check that their mate (using the ALT allele) are 
      the same too
      Default: false
    -c, --contig
      limit to this contig
    -x, --exclude
      Exclude regions in this bed file
    --force-svtype
      When comparing two SV variants, their INFO/SVTYPE should be the same. 
      Default is to just use coordinates to compare non-BND variants.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --no-bnd
      discar BND
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --sv-alleles-bases
      When comparing two non-BND SV variants, use their ALT alleles to adjust 
      the interval. It solves the problem of  
      'chr2:10556028:AATTATATAATTAAATTAATTATATAATT:A'  vs 
      'chr2:10556028:A:AATTATATAATTAAATTAATTATATAATT'. See 
      https://twitter.com/yokofakun/status/1169182491606999046 
      Default: false
    --sv-fraction
      Two SV have are the same if they share a fraction 'x' of their bases. 
      For very small SV the fraction can be quite small while for large SV the 
      fraction should be close to 1. The Syntax is the following : 
      (<MAX_SIZE_INCLUSIVE>:<FRACTION as double or percent>;)+ . For example 
      if the SV as a size of 99bp, the fraction used with be 0.6 for 
      '10:0.1;100:0.6;1000:0.9'. For the smallest size, a simple overlap is a 
      positive match.
      Default: 10:0.5;100:0.75;1000:0.8;10000:0.9
    --version
      print version and exit

Keywords

• sv
• manta
• vcf

Creation Date

20190916

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/manta/MantaMerger.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/manta/MantaMergerTest.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 mantamerger ? 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

input is a list of indexed vcf files or one file with the ‘.list’ suffix containing the path to the vcfs

Example

$ find src -name "manta*z" > jeter.list
$ java -jar dist/mantamerger.jar jeter.list 2> /dev/null

(...)

This site is open source. Improve this page.