jvarkit

VcfSetSequenceDictionary

Set the ##contig lines in a VCF header on the fly

Usage

Usage: vcfsetdict [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].
    -n, --onNotFound
      Contig converter. I will do my best to convert the contig names (e.g 
      'chr1' -> '1'): But what should I do when comparing two dictionaries 
      with different notations
      Default: SKIP
      Possible Values: [RAISE_EXCEPTION, SKIP, RETURN_ORIGINAL]
    -o, --out
      Output file. Optional . Default: stdout
  * -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit

Keywords

• vcf
• dict
• fai

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 vcfsetdict

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

Creation Date

20140105

Source code

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

Unit Tests

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

The tool will try to convert the contig names (‘1’ -> ‘chr1’) according to the new dictionary.

Example

java  -jar jvarkit-git/vcfsetdict.jar --onNotFound SKIP -r ref.fasta input.vcf > out.vcf

History

• [20170906] remove the creation of a dictionary, moved to VcfCreateDictionary

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