jvarkit

IndexCovToSV

same as indexcov2vcf but merge segments

Usage

Usage: indexcov2sv [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
    -d, --distance
      Merge segment if they are within that distance. A distance specified as 
      a positive integer.Commas are removed. The following suffixes are 
      interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 0
    --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
    -norm, --norm
      normalize: only one ALT allele per variant
      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 CreateSequenceDictionary
    --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

Compilation

Requirements / Dependencies

• java compiler SDK 11. 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 "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew indexcov2sv

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

Creation Date

20200228

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/indexcov/IndexCovToSV.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 indexcov2sv ? 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

Same as indexcov2sv but merge contigous segments.

Input

input is a tab-delimited file created by e.g: indexcov (https://github.com/brentp/goleft/tree/master/indexcov)

#chrom  start  end     SampleBB  SampleBC  SampleBD  SampleBE  SampleBF  SampleBG  SampleBH
chr1    23778  40778   1.59      1.31      1.67      1.61      1.83      1.52      1.48
chr1    29106  46106   1.9       1.54      1.72      1.97      1.88      1.53      1.95
chr1    84581  101581  0.764     0.841     1.2       1.16      1.18      1.13      1.23
chr1    15220  32220   0.355     0.704     1.09      0.784     0.81      1.37      0.954
chr1    58553  75553   0.353     0.436     0.912     0.836     1.16      1.09      0.611
chr1    19347  36347   0.381     0.411     0.811     0.795     1.16      1.22      0.495
chr1    81062  98062   1.09      0.972     1.35      1.22      1.66      1.76      1.1
chr1    17353  34353   1.06      1.06      1.23      1.26      1.44      1.43      1.03
chr1    48498  65498   1.08      0.996     1.28      1.44      1.52      1.57      1.05

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