VcfAlleleToSymbolic

Last commit

Convert large IUPAC allele to symbolic

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfallele2symbolic  [options] Files

Usage: vcfallele2symbolic [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --keep-ref
      do not replace the REF allele
      Default: false
    -n, --length
      Change allele if the length it greater or equal to that value
      Default: 10
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

  • vcf
  • allele
  • snv
  • vcf

Creation Date

20250717

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfallele2symbolic/VcfAlleleToSymbolic.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfallele2symbolic/VcfAlleleToSymbolicTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfallele2symbolic ? 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

for SV vcf alleles, the annotation with VEP can be heavy if the alleles are coded as loarge IUPAC string

Example

java -jar dist/jvarkit.jar vcfallele2symbolic   in.vcf > out.vcf