jvarkit

SamShortInvertion

Scan short inversions in reads.

Usage

Usage: java -jar dist/samshortinvert.jar  [options] Files
Usage: samshortinvert [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
    --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].
    --mapq
      min mapping quality
      Default: 1
    --min-inversion-length
      min inversion length
      Default: 8
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit

Keywords

• sam
• bam
• sv
• inversion

Compilation

Requirements / Dependencies

• java compiler SDK 17. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone --recurse-submodules "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew samshortinvert

The java jar file will be installed in the dist directory.

Creation Date

20140228

Source code

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

finds the regions having some short inversions.

output is a VCF file

Example:

$ java -jar ${JVARKIT_DIST}/samshortinvert.jar -R ref.fasta bams.list |\
 	bcftools view -i 'INFO/DPMAX>10' > out.vcf

This site is open source. Improve this page.