DictToVcf

convert a SAM dictionary from vcf,sam,bam,dict, etc.. to vcf.

Usage

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

Usage: java -jar dist/jvarkit.jar dict2vcf  [options] Files

Usage: dict2vcf [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
    --extra-lines
      File containing extra header lines
    --format, --formats
      Add those predefined FORMAT fields
      Default: GT,GQ,DP,PL,AD,FT,PS,PQ
    --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].
    --info, --infos
      Add those predefined INFO fields
      Default: END,DB,DP,SB,AF,AC,AN,MQ0,MQ,SOMATIC
    -o, --out
      Output file. Optional . Default: stdout
    --samples
      Add those samples
      Default: []
    --samples-file
      Read samples from file. If the file has a BAM/CRAM/BCF/VCF extension, 
      samples are extracted from their metadata.
    --version
      print version and exit

Keywords

• dict
• bed
• sam
• bam
• vcf

Creation Date

20251126

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/dict2vcf/DictToVcf.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/dict2vcf/DictToVcfTest.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 dict2vcf ? 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

Motivation

convert Dict to VCF when you want to generate an empty vcf file

Example

java -jar dist/jvarkit.jar dict2vcf src/test/resources/human_b37.dict  --samples S1,S3