VcfConcat

Concatenate VCFs. See also bcftools concat

Usage

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

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

Usage: vcfconcat [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
    -R, --dict
      Optional: use that dictionary otherwise, use the first ddictionary found 
      in the vcfs.A SAM Sequence dictionary source: it can be a *.dict file, a 
      fasta file indexed with 'picard CreateSequenceDictionary' or 'samtools 
      dict', or any hts file containing a dictionary (VCF, BAM, CRAM, 
      intervals...) 
    -G, --drop-genotypes
      Drop genotypes
      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].
    --merge
      merge all samples. First Scan all files to get all distinct samples
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --bed, --regions-file, --regions
      limit to that bed file
    -S, --samples
      Print Samples in INFO columns. implies --drop-genotypes
      Default: none
      Possible Values: [none, all, with_alt]
    -T, --tag
      if not empty, add INFO/tag containing the source/path of the variant
      Default: <empty string>
    --version
      print version and exit

Keywords

• vcf

Creation Date

20131230

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfconcat/VcfConcat.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 vcfconcat ? 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

find /path -type f -name "*.vcf.gz" > input.list
java -jar jvarkit.jar vcfconcat --merge input.list

if not argument: paths are read on stdin:

find /path -type f -name "*.vcf.gz" |\
    java -jar jvarkit.jar vcfconcat --merge input.list