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MergeVcfs (Picard)

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

Category Variant Manipulation


Overview

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
 

MergeVcfs (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Arguments
--INPUT
 -I
[] VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files, one per line.
--OUTPUT
 -O
null The merged VCF or BCF file. File format is determined by file extension.
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--help
 -h
false display the help message
--SEQUENCE_DICTIONARY
 -D
null The index sequence dictionary to use instead of the sequence dictionary in the input files
--version
false display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL
5 Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX
true Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE
false Whether to create an MD5 digest for any BAM or FASTQ files created.
--GA4GH_CLIENT_SECRETS
client_secrets.json Google Genomics API client_secrets.json file path.
--MAX_RECORDS_IN_RAM
500000 When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--TMP_DIR
[] One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER
 -use_jdk_deflater
false Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER
 -use_jdk_inflater
false Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY
STRICT Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  true


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--INPUT / -I

VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files, one per line.

R List[File]  []


--MAX_RECORDS_IN_RAM / NA

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--OUTPUT / -O

The merged VCF or BCF file. File format is determined by file extension.

R File  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--SEQUENCE_DICTIONARY / -D

The index sequence dictionary to use instead of the sequence dictionary in the input files

File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []


--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false


--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false


--VALIDATION_STRINGENCY / NA

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  STRICT


--VERBOSITY / NA

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.0.4.0 built at 23-40-2018 11:40:56.