jvarkit

NoZeroVariationVCF

cat a whole VCF, or, if there is no variant, creates a fake one

Usage

Usage: nozerovariationvcf [options] Files
  Options:
    -f, --filter
      FILTER name
      Default: FAKESNP
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -R, -r, --reference
      The parameter is the path to an Indexed fasta Reference file. This fasta 
      file must be indexed with samtools faidx and with picard 
      CreateSequenceDictionary. The parameter can also be a 'key' (matching 
      the regular expression `[A-Za-z][A-Za-z0-9_\\-]*`) in a catalog file. A 
      'catalog' file is a java property file ( 
      https://docs.oracle.com/javase/tutorial/essential/environment/properties.html 
      ) where the values are the path to the fasta file.  Catalogs are 
      searched in that order : `${PWD}/fasta-ref.properties`, 
      `${HOME}/.fasta-ref.properties`, `/etc/jvarkit/fasta-ref.properties`.  
      If the key or the path are not defined by the user, they will be 
      searched in that order 1) the java property 
      -Djvarkit.fasta.reference=pathTofastaOrCatalogKey . 2) the linux 
      environement variable $FASTA_REFERENCE=pathTofastaOrCatalogKey 3) The 
      catalogs. 
      Default: <<Default Fasta Reference Supplier>>
    --version
      print version and exit

Keywords

• vcf

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 nozerovariationvcf

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/NoZeroVariationVCF.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/NoZeroVariationVCFTest.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 nozerovariationvcf ? 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

# we use grep to create an empty VCF
$ gunzip -c file.vcf.gz | \
 grep  "#" |\
 java -jar dist/nozerovariationvcf.jar -r human_g1k_v37.fasta

##fileformat=VCFv4.1
##FILTER=<ID=FAKESNP,Description="Fake SNP created because vcf input was empty. See https://github.com/lindenb/jvarkit">
(...)
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
GL000207.1	1	.	C	A	1	FAKESNP	.	GT:DP:GQ	0/1:1:1

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