jvarkit

HaloplexParasite

for @SolenaLS : remove artctifacts from haloplex that gives indels in GATK hapcaller

Usage

Usage: haloplexparasite [options] Files
  Options:
    -B, --bams
      A list of path to indexed BAM files
    -m, --clipsize
      Min. Soft Clipping size
      Default: 10
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -t, --treshold
      treshold
      Default: 5.0E-4
    --version
      print version and exit

Keywords

• vcf
• haloplex

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 haloplexparasite

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/haloplex/HaloplexParasite.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 haloplexparasite ? 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

Examples

echo "input.bam" > all.list
gunzip -c input.vcf.gz |
  java -jar dist/haloplexparasite.jar -B all.list
rm all.list

Examples

echo "input.bam" > all.list
gunzip -c input.vcf.gz |
  java -jar dist/haloplexparasite.jar -B all.list
rm all.list

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