@DocumentedFeature
public class MergeVcfs
extends CommandLineProgram

Combines multiple variant files into a single variant file.

Inputs

• One or more input file in VCF format (can be gzipped, i.e. ending in ".vcf.gz", or binary compressed, i.e. ending in ".bcf").
• Optionally a sequence dictionary file (typically name ending in .dict) if the input VCF does not contain a complete contig list and if the output index is to be created (true by default).

The input variant data must adhere to the following rules:

• If there are samples, those must be the same across all input files.
• Input file headers must be contain compatible declarations for common annotations (INFO, FORMAT fields) and filters.
• Input files variant records must be sorted by their contig and position following the sequence dictionary provided or the header contig list.

You can either directly specify the list of files by specifying INPUT multiple times, or provide a list in a file with name ending in ".list" to INPUT.

Outputs

A VCF sorted (i) according to the dictionary and (ii) by coordiante.

Usage examples

Example 1:

We combine several variant files in different formats, where at least one of them contains the contig list in its header.

     java -jar picard.jar MergeVcfs \
          I=input_variants.01.vcf \
          I=input_variants.02.vcf.gz \
          O=output_variants.vcf.gz
 

Example 2:

Similar to example 1 but we use an input list file to specify the input files:

     java -jar picard.jar MergeVcfs \
          I=input_variant_files.list \
          O=output_variants.vcf.gz