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Peek annotations from gnomad


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

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

Usage: vcfgnomad [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
      When we're looking for variants 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,g,gb
      Default: 10000
    -F, --fields
      AF fields to peek-up from gnomad. Space/comma/semicolon separated
      Default: AF_popmax,AF_nfe
      Generate MD5 checksum for VCF output.
      Default: false
  * -g, --gnomad
      Path to Indexed Gnomad VCF file. Or a file with the '.list' suffix 
      containing the path to the indexed VCFs (one per contig).
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
      Max allele frequency
      Default: 1.0
      Min allele frequency
      Default: 0.0
      do Not Update ID if it is missing in user's variant
      Default: false
      is the genome vcf exome or genome ? If 'undefined', try to guess from 
      Default: undefined
      Possible Values: [genome, exome, undefined]
    -o, --out
      Output file. Optional . Default: stdout
      If not empty, include the Gnomad FILTERs using this prefix.
      Default: GNOMAD
      print version and exit


Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite vcfgnomad ? 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

The tool was redesigned on July 2nd, 2020.


java -jar dist/vcfgnomad.jar -g src/test/resources/gnomad.genomes.r2.0.1.sites.1.vcf.gz src/test/resources/test_vcf01.vcf