VcFilterGenes

Last commit

Filter VEP/SnpEff Output from a list of genes.

Usage

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

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

Usage: vcffiltergenes [options] Files
  Options:
    -a, --add
      [20180627] Gene Names: Add this gene, multiple separated by 
      comma,spaces,semicolon 
      Default: <empty string>
    --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
    -filter, --filter
      If empty: remove the variants from the VCF. If not empty, add a token in 
      the column FILTER.
      Default: <empty string>
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -g, --genes
      Gene/transcript file: one name per line
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

  • gene
  • vcf
  • vep
  • snpeff

See also in Biostars

Creation Date

20160322

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcffiltergenes/VcFilterGenes.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcffiltergenes ? 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

echo "IL2" > genes.txt
echo "NOCTH2" >>  genes.txt
gunzip -c input.vcf.gz |\
    java -jar dit/vcfburdenfiltergenes.jar -g genes.txt

Example

$ wget -O - -q "https://github.com/immune-health/antigen.garnish/raw/f0453336a4859c83d27640c286d3960c1672f164/inst/extdata/testdata/antigen.garnish_hg19anno_example.vcf"  |\
    grep -w 216371854  | cut -f 8 | tr ";" "\n"   | grep ^ANN= | cut -c5- | tr "," "\n"
T|missense_variant|MODERATE|USH2A|USH2A|transcript|NM_206933.2|protein_coding|18/72|c.3884G>A|p.Arg1295Gln|4271/18883|3884/15609|1295/5202||
T|missense_variant|MODERATE|USH2A|USH2A|transcript|NM_007123.5|protein_coding|18/21|c.3884G>A|p.Arg1295Gln|4271/6316|3884/4641|1295/1546||

$ wget -O - -q "https://github.com/immune-health/antigen.garnish/raw/f0453336a4859c83d27640c286d3960c1672f164/inst/extdata/testdata/antigen.garnish_hg19anno_example.vcf"  |\
    sed 's/PASS\t[A-Z0-9]*;/PASS\t/' |\ ## the vcf above is malformed, quick hack
    java -jar dist/jvarkit.jar vcffiltergenes.jar -a "NM_206933.2" |\
    grep -w 216371854  | cut -f 8 | tr ";" "\n"   | grep ^ANN= | cut -c5- | tr "," "\n"
T|missense_variant|MODERATE|USH2A|USH2A|transcript|NM_206933.2|protein_coding|18/72|c.3884G>A|p.Arg1295Gln|4271/18883|3884/15609|1295/5202||