jvarkit

SVCasesControls

Find SV present in cases but not in controls.

Usage

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

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

Usage: svcasescontrols [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --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
    --complex
      By default this tool select the SV that are found in the cases but not 
      in the controls. When using this flag, all variants for cases are 
      extracted and a count of CASE/CONTROL having the SV is added in the INFO 
      column. 
      Default: false
    -c, --contig, --chrom
      limit to this contig
    --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
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      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-overlap-fraction
      Two CNV/DEL/.. variants are the same if they share 'x' fraction of their 
      size. 
      Default: 0.75
    --sv-small-overlap
      Two non-BND variants are the same if they overlap and both have a 
      length<= 'x'. A distance specified as a positive integer.Commas are 
      removed. The following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 10
    --version
      print version and exit

Keywords

• sv
• manta
• vcf

Creation Date

20240513

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/SVCasesControls.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 svcasescontrols ? 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

Find SV present in cases and controls.

Input

input is a tab delimited file with a header:

• vcf: the path to the vcf
• sample : the sample name associated to the vcf. If empty the name will be searched in the CHROM header
• status : case OR control

Example

 $ java -jar jvarkit.jar svcasescontrols input.tsv > output.vcf

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