jvarkit

VcfRemoveGenotypeIfInVcf

Reset Genotypes in VCF (./.) if they’ve been found in another VCF indexed with tabix

Usage

Usage: vcfresetvcf [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
  * -t, --tabix
      Tabix indexed VCF file
    --version
      print version and exit
    -x
      remove variant if there is no called genotype
      Default: false

Keywords

• vcf
• genotype

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 vcfresetvcf

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/VcfRemoveGenotypeIfInVcf.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 vcfresetvcf ? 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

$ gunzip -c input.vcf.gz | grep -E '1308871'
1	1308871	.	A	T	6.2	.	.	GT:PL:DP:GQ	1/1:35,3,0:1:4



$ gunzip -c input.vcf.gz | grep -E '(^#|1308871)' |\
  java -jar dist/vcfresetvcf.jar -x ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz |\
  grep -v '^#'
1	1308871	.	A	T	6.20	.	.	GT	./.

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