jvarkit

VcfStretchOfGt

Last commit

Try to finds deletion by searching strech of HOM_REF/HOM_VAR/NO_CALL Genotypes.

Usage

Usage: vcfstrechofgt [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -p, --pedigree
      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
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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/VcfStretchOfGt.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/VcfStretchOfGtTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfstrechofgt ? 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

Example

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

#chrom	start0	end0	length	count.affected.variants	average.affected.depth	count.other.variants
1	870316	870317	1	1	5.0	0
1	919500	919501	1	1	0.0	0
1	963703	963704	1	1	0.0	0
1	1004201	1004202	1	1	0.0	0