VCFBigWig

Annotate a VCF with values from a bigwig file

Usage

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

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

Usage: vcfbigwig [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
  * -B, --bigwig
      Path/URI to bigwig file.
    --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, -tag
      Name of the INFO tag. default: name of the bigwig
    --version
      print version and exit

Keywords

• vcf
• wig
• wiggle
• bigwig

Creation Date

20200506

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfbigwig/VCFBigWig.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 vcfbigwig ? 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

 java -jar dist/vcfbigwig.jar \
    -T GERP \
    -B gerp.bw input.vcf.gz 

##INFO=<ID=GERP,Number=1,Type=Float,Description="Values from bigwig file: com.github.lindenb.jvarkit.tools.vcfbigwig.VCFBigWig BIGWIG=gerp.bw TAG=GERP IN=input.vcf.gz    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO(...)
A   33926   .   G   A   182 .   GERP=-6.35(...)
A   45365   .   A   G   222 .   GERP=-3.55(...)