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Peek the AF from another VCF


Usage: vcfpeekaf [options] Files
      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, --buffer-size
      When we're looking for variant in a lare VCF file, load the variants in 
      an interval of 'N' bases instead of doing a random access for each 
      variant. A distance specified as a positive integer.Commas are removed. 
      The following suffixes are interpreted : b,bp,k,kb,m,mb
      Default: 10000
  * -F, --database, --tabix, --resource
      An indexed VCF file. Source of the annotations
    -f, --filter
      soft FILTER the variant of this data if AF is not found or it greater > 
      max-af or lower than min-af. If empty, just DISCARD the variant
      Default: <empty string>
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
    -l, --list
      List available AF peekers and exit.
      AF min treshold. Variant is accepted is computed AF >= treshold.
      Default: 0.0
      Do not look at the alternate alleles concordance
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
      Peek database variant ID if it is missing in the processed VCF.
      Default: false
    -P, --peek-info
      Name of INFO tag in the vcf database to extract the AF value for 
      exractor .'Custom'
  * -p, --peeker
      AF Peeker name. Use option --list to get a list of peekers.
    -T, --tag
      INFO tag to put found frequency. empty: no extra tag.
      Default: <empty string>
  * -t, --treshold, --max-af
      AF max treshold. Variant is accepted is computed AF <= treshold.
      Default: 1.0
      print version and exit



Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfpeekaf

The java jar file will be installed in the dist directory.

Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite vcfpeekaf ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030