CombineGenotypingArrayVcfs takes one or more VCF files, as generated by GtcToVcf and combines them into a single VCF. The input VCFs must have the same sequence dictionary and same list of variant loci. The input VCFs must not share sample Ids.

Usage example:

java -jar picard.jar CombineGenotypingArrayVcfs \
      INPUT=input1.vcf \
      INPUT=input2.vcf \
      OUTPUT=output.vcf

Category Genotyping Arrays Manipulation

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Overview

A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci. The input files must not share sample Ids. The input files must have the same contig lists. Throws IllegalArgumentException if the contig lists are not present in the input files, or are not identical this class uses the GATK to merge headers, which may throw exceptions if the headers cannot be merged. See VCFUtils.smartMergeHeaders for details.

An index file is created for the output file by default. Using an output file name with a ".gz" extension will create gzip-compressed output. Note that this tool is written to handle a use case not supported by MergeVcfs (merging multiple VCFs, each for a different sample). Note also that this tool is similar intent to the GATK tool CombineVariants (which is in GATK3, but not in 4). There are some array-specific features in this tool that probably could be generalized in CombineVariants when/if that is installed in GATK4.

CombineGenotypingArrayVcfs (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		Input VCF file(s).
--OUTPUT  -O		Output VCF file.
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
--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 an index when writing VCF or coordinate sorted BAM output.
--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		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.

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--arguments_file

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

List[File]  []

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--COMPRESSION_LEVEL

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

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean  true

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--CREATE_MD5_FILE

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

boolean  false

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--GA4GH_CLIENT_SECRETS

Google Genomics API client_secrets.json file path.

String  client_secrets.json

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--help / -h

display the help message

boolean  false

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--INPUT / -I

Input VCF file(s).

R List[File]  []

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--MAX_RECORDS_IN_RAM

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  [ [ -∞  ∞ ] ]

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--OUTPUT / -O

Output VCF file.

R File  null

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--QUIET

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

Boolean  false

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--TMP_DIR

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

List[File]  []

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--USE_JDK_DEFLATER / -use_jdk_deflater

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

Boolean  false

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--USE_JDK_INFLATER / -use_jdk_inflater

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

Boolean  false

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--VALIDATION_STRINGENCY

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

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--VERBOSITY

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

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--version

display the version number for this tool

boolean  false

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GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.