VcfRebase

Last commit

Restriction sites overlaping variations in a vcf

Usage

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

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

Usage: vcfrebase [options] Files
  Options:
    -A, --attribute
      VCF INFO attribute
      Default: ENZ
    --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
    -E, -enzyme, --enzyme
      restrict to that enzyme name. Default: use all enzymes
      Default: []
    --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].
    -o, --out
      Output file. Optional . Default: stdout
    -R, -reference, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit
    -w, -weight, --weight
      min enzyme weight 6 = 6 cutter like GAATTC, 2 = 2 cutter like ATNNNNNNAT
      Default: 5.0

Keywords

vcf
rebase
restriction
enzyme

Creation Date

20131115

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfrebase/VcfRebase.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfrebase/VcfRebaseTest.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 vcfrebase ? 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/vcfrebase.jar -w 6 -R ~/data/human_g1k_v37.fasta src/test/resources/test_vcf01.vcf | bcftools annotate -x '^INFO/ENZ' | bcftools view --drop-genotypes | grep ENZ

INFO=

bcftools_annotateCommand=annotate -x ^INFO/ENZ; Date=Wed Nov 13 10:38:39 2019