jvarkit

VcfAlleleBalance

Last commit

Insert missing allele balance annotation using FORMAT:AD

Usage

Usage: vcfallelebalance [options] Files
  Options:
    -f, --filtered
      ignore FILTER-ed **GENOTYPES**
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -p, -ped, --pedigree, --ped
      A pedigree is a text file delimited with tabs. No header. Columns are 
      (1) Family (2) Individual-ID (3) Father Id or '0' (4) Mother Id or '0' 
      (5) Sex : 1 male/2 female / 0 unknown (6) Status : 0 unaffected, 1 
      affected,-9 unknown
    -s, --snp
      consider only snps
      Default: false
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfallelebalance

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/misc/VcfAlleleBalance.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/VcfAlleleBalanceTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfallelebalance ? 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

August 2018, for @MKarakachoff

part of the code was inspired from GATK public code : https://github.com/broadgsa/gatk-protected/blob/master/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java

Example

$ java -jar dist/vcfallelebalance.jar  src/test/resources/test_vcf01.vcf
$ java -jar dist/vcfallelebalance.jar -p src/test/resources/test_vcf01.ped src/test/resources/test_vcf01.vcf