jvarkit

NaiveCnvDetector

experimental CNV detection for multiple samples.

Usage

Usage: naivecnvdetector [options] Files
  Options:
    -c, --config
      config file. Tab delimited. 
      Sample-name(tab)mean-depth(tab)integer[affected=1,non-affected=0]. If 
      this file is not specified , all samples are considered unaffected 
      (discovery mode).
    -E, -del, --del, --deletion
      Deletion Treshold. Which fraction of the median depth is considered as 
      aa deletion. Must be <1.0
      Default: 0.5
    --disable-consecutive
      Disable 'consecutive' positions criteria. Default: dump buffer of 
      position if the current samtools-depth line is not the very next 
      expected position.
      Default: false
    -U, -dup, --dup, --duplication
      Duplication Treshold. Which fraction of the median depth is considered 
      as a duplication. Must be >1.0
      Default: 1.5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -md, --min-dp
      At least one 'unaffected' sample must have a normalized-depth greater 
      than this value.
      Default: 20
    --no-both
      There cannot be a DEL and a DUP at the same place.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    -stddevu, --stddev-unaffected
      Maximum standard deviation of depth for unaffected samples. Ignored if 
      negative or if not any affected samples is defined.
      Default: 10.0
    --version
      print version and exit
    --weirdDepth
      Treat normalized depth greater than this value as 'weird' and discard 
      the sliding windows at this place.
      Default: 500
    -R, -reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -s
      window shift
      Default: 500
    -t
      DEL must be < median-depth-stdev and DUP must be > median-depth+stdev
      Default: false
    -w
      window size
      Default: 1000

Keywords

• cnv
• bam
• sam
• wig
• bigwig
• bigbed

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 naivecnvdetector

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

Source code

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

Unit Tests

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

Input is either:

• one fileof samtools depth output. All ‘N’ samples in one file.
• ‘N’ files (samtools depth output AND/OR bigwig/bigbed [experimental not tested] ). One samples in per file. REF dictionary is required. List of file can be specified if input ends with ‘.list’

bigbed and bigwig have not been tested; Bigbed shouldn’t have overlapping regions…

Example

samtools depth -r '1:1234-567' *.bam |\
	java -jar dist/naivecnvdetector.jar  > out.tsv

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