VcfGnomad

Peek annotations from gnomad

Usage

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
  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
    --bufferSize
      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
    --disable-bad-flag
      A list of INFO/xxx Flag that will be used to FILTER variants. Multiple, 
      comma separated: valid values are 
      'lcr,segdup,fail_interval_qc,negative_train_site'. 
      Default: <empty string>
    -F, --fields
      AF fields to peek-up from gnomad. Space/comma/semicolon separated
      Default: AF_popmax,AF_nfe
    --generate-vcf-md5
      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
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --max-af
      Max allele frequency
      Default: 1.0
    --min-af
      Min allele frequency
      Default: 0.0
    --noUpdateId
      do Not Update ID if it is missing in user's variant
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --prefix
      Use this prefix for the FILTERs.
      Default: GNOMAD
    --skip-filtered, --pass
      Remove any user's variant if the gnomad variant is filtered (or overlap 
      a LCR,segdup, ...), or doesn't fit the min/max AF
      Default: false
    --version
      print version and exit

Keywords

• vcf
• annotation
• gnomad

Creation Date

20170407

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gnomad/VcfGnomad.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/gnomad/VcfGnomadTest.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 vcfgnomad ? 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

The tool was redesigned on July 2nd, 2020.

Example:

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