jvarkit

ScanStructuralVariants

Scan structural variants for case/controls data

Usage

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

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

Usage: scansv [options] Files
  Options:
    --all
      Print all original variants from each file instead of printing just one.
      Default: false
    --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
    --bed
      A source of intervals. The following suffixes are recognized: vcf, 
      vcf.gz bed, bed.gz, gtf, gff, gff.gz, gtf.gz.Otherwise it could be an 
      empty string (no interval) or a list of plain interval separated by '[ 
      \t\n;,]' 
    --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, --controls
      Controls indexed VCF files. a file endings with the suffix '.list' is 
      interpretted as a list of path.
      Default: []
    --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].
    -L, --large
      Large number of controls: By default, all VCF readers for controls are 
      opened and are kept opened. It's fast but requires a lot of resources. 
      This option open+close the controls if needed but it makes things 
      slower. It's the number of VCF that should be keept open, So '0' = 
      ignore/all re-open+close (slow)
      Default: 0
    --maf
      Max frequency of variants found in controls. 0:no control should carry 
      the variant
      Default: 0.0
    -o, --out
      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

• cnv
• indel
• sv
• pedigree

Creation Date

20190815

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/ScanStructuralVariantsTest.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 scansv ? 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

Example

find CONTROLS/ -name "*.vcf.gz" > controls.list

java -Xmx3g -Djava.io.tmpdir=. -jar scansv.jar --controls controls.list -d2 25  cases1.vcf cases2.vcf > out.vcf

This site is open source. Improve this page.