jvarkit

VcfRemoveUnusedAlt

Remove unused ALT allele if there is no genotype with this alt, or there is no sample but AC=0

Usage

Usage: vcfremoveunusedalt [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -neverspan, --neverspan
      Remove ALL spanning deletions '*'. VCF must have no genotype.
      Default: false
    -onespan, --onespan
      Don't print the variant if the only remaining allele is  '*'
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

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 vcfremoveunusedalt

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/VcfRemoveUnusedAlt.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/VcfRemoveUnusedAltTest.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 vcfremoveunusedalt ? 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

when using gatk SelectVariants with sample names (-sn) some alleles specific of the samples than have been removed, remain in the vcf.

SNPEFF / VEP

this tool removes unused annotations from SNPEFF(ANN=) and VEP.

Example

$ cat in.vcf
(...)
chr1	7358	.	ACTT	*,A	1313.61	PASS	AC=0,10;AF=0,0.005828;AN=1716

$ java -jar dist/vcfremoveunusedalt.jar  in.vcf | grep -w 17358 -m1
chr1	7358	.	ACTT	A	1313.61	PASS	AC=10;AF=0.005828;AN=1716

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