jvarkit

IndexCovToVcf

convert indexcov data to vcf

Usage

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

Usage: java -jar dist/jvarkit.jar indexcov2vcf  [options] Files

Usage: indexcov2vcf [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
    --cases
      File or comma-separated list of control samples
    --controls
      File or comma-separated list of control samples
    --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].
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    --no-merge
      disable adjacent block merging for the same variant (keep the original 
      bed structure)
      Default: false
    -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
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    -t, --treshold
      DUP if 1.5-x<=depth<=1.5+x . HET_DEL if 0.5-x<=depth<=0.5+x HOM_DEL if 
      0.0-x<=depth<=0.0+x.. A decimal number between 0.0 and 1.0. If the value 
      ends with '%' it is interpretted as a percentage eg. '1%' => '0.01'. A 
      slash '/' is interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.05
    --version
      print version and exit

Keywords

• cnv
• duplication
• deletion
• sv
• indexcov

Creation Date

20200528

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/indexcov/IndexCovToVcfTest.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 indexcov2vcf ? 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

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