VCFSplitVEP

Last commit

Split CSQ vep annotations

Usage

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

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

Usage: vcfsplitvep [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
    --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].
    -o, --out
      Output file. Optional . Default: stdout
    -t, --tag, --tags
      VEP tags name{:type{:aggregate}},name2{:type2{:aggregate2}},etc...  
      where type is a VCF info type Integer,String,Float an aggregate is one 
      of none,min,max,uniq,first,random
      Default: []
    --version
      print version and exit