VCFNearest

Last commit

find nearest feature near a variant

Usage

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

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

Usage: vcfnearest [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
  * -B, --bed
      Bed path.
  * -C, --columns
      comma separated names of the columns in the bed file. Empty columns will 
      be skipped. e.g: ',,,NAME,TYPE,,SCORE' expects a bed with 7 columns. The 
      1,2,3 and 6th will be skipped. Two columns are added: the side (0: 
      overlap, -1 bed is before variant , 1 bed is after variant ) and the 
      distance 
      Default: <empty string>
    -d, --distance
      max distance from variant to feature. A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb,g,gb 
      Default: 0
    --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].
    -n, --max-features
      do not print more than 'x' features; disable if x <=0
      Default: -1
    -o, --out
      Output file. Optional . Default: stdout
    --tabix
      use tabix index if possible (otherwise, put the bed in memory)
      Default: false
    -t, --tag
      Tag name
      Default: NEAREST
    --version
      print version and exit

Keywords

vcf
vep
annotation

Creation Date

20250523

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfnearest/VCFNearest.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfnearest/VCFNearestTest.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 vcfnearest ? 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