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:
    -a, --affected
      Same as option --pedigree but provide the name of the samples using a 
      comma/space/semicolon separated string
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -nc, --no-call
      Do not accept NO_CALL genotypes.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -p, --pedigree
      If defined, the tool will use the affected sample and find strech where 
      all affected could be a DEL.A pedigree file. tab delimited. Columns: 
      family,id,father,mother, sex:(0:unknown;1:male;2:female), phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    --version
      print version and exit

Keywords

vcf
deletion
cnv

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 vcfstrechofgt

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

Creation Date

20190103

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

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 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