jvarkit

VCFBigWig

Annotate a VCF with values from a bigwig file

Usage

Usage: java -jar dist/vcfbigwig.jar  [options] Files
Usage: vcfbigwig [options] Files
  Options:
    -a, --aggregate
      How to aggregate overlapping values: 'avg' average; 'median': median, 
      'first': use first, 'all' : print all the data
      Default: avg
      Possible Values: [avg, median, first, all]
    --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 to the bigwig file. [20180122] If the path ends with '.xml' it is 
      interpretted as a XML file containing describing a set of BigWig 
      resources; See online doc.
    -C, --contained
      Specifies wig values must be contained by region. if false: return any 
      intersecting region values
      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, -tag
      Name of the INFO tag. default: name of the bigwig
    --version
      print version and exit

Keywords

• vcf
• wig
• wiggle
• bigwig

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfbigwig

The java jar file will be installed in the dist directory.

Creation Date

20200506

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfbigwig/VCFBigWigTest.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

XML definition

multiple BigWig files can be specified using a XML file.

• Root is <registry>
• under <registry> is a set of `' elements.
• under <bigwig> contains the <uri>'(required) , ` and ``

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(...)

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