Gathers multiple VCF files from a scatter operation into a single VCF file

Category Variant Manipulation

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Overview

This tool combines together rows of variant calls from multiple VCFs, e.g. those produced by scattering calling across genomic intervals, into a single VCF. This tool enables scattering operations, e.g. in the cloud, and is preferred for such contexts over Picard MergeVcfs or Picard GatherVCfs. The tool also runs locally.

The input files need to have the same set of samples but completely different sets of loci. These input files must be supplied in genomic order and must not have events at overlapping positions.

Input

A set of VCF files, each specified in genomic order with the -I option, or a .list text file listing the set of VCFs to be merged, one file per line.

Output

A single VCF file containing the variant call records from the multiple VCFs.

Usage examples

Specify each VCF file within the command.

 gatk GatherVcfsCloud \
     -I cohortA_chr1.vcf.gz \
     -I cohortA_chr2.vcf.gz \
     -O cohortA_chr1chr2.vcf.gz
 

Specify the VCF files using the following input.list:

     cohortA_chr1.vcf.gz
     cohortA_chr2.vcf.gz
 

 gatk GatherVcfsCloud \
     -I input.list
     -O cohortA_chr1chr2.vcf.gz
 

GatherVcfsCloud 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	null	Output VCF file.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--cloud-prefetch-buffer  -CPB	2	Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--create-output-variant-index  -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--gather-type	AUTOMATIC	Choose which method should be used to gather: BLOCK gathering is faster but onlyworks when you have both bgzipped inputs and outputs, while CONVENTIONAL gather is much slower but should work on all vcf files. AUTOMATIC chooses BLOCK if possible and CONVENTIONAL otherwise.
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays	""	Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help  -h	false	display the help message
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file	null	A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir	null	Temp directory to use.
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--disable-contig-ordering-check	false	Don't check relative ordering of contigs when doing a conventional gather
--ignore-safety-checks	false	Disable sanity checks to improve performance, may result in silently creating corrupted outputs data
--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 / NA

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

List[File]  []

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--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  2  [ [ -∞  ∞ ] ]

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--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

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--disable-contig-ordering-check / NA

Don't check relative ordering of contigs when doing a conventional gather

boolean  false

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--gather-type / NA

Choose which method should be used to gather: BLOCK gathering is faster but onlyworks when you have both bgzipped inputs and outputs, while CONVENTIONAL gather is much slower but should work on all vcf files. AUTOMATIC chooses BLOCK if possible and CONVENTIONAL otherwise.

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

BLOCK

CONVENTIONAL

AUTOMATIC

GatherType  AUTOMATIC

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--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

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--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""

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--help / -h

display the help message

boolean  false

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--ignore-safety-checks / NA

Disable sanity checks to improve performance, may result in silently creating corrupted outputs data

boolean  false

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--input / -I

Input VCF file(s).

R List[String]  []

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--output / -O

Output VCF file.

R File  null

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--QUIET / NA

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

Boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--tmp-dir / NA

Temp directory to use.

String  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--verbosity / -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 / NA

display the version number for this tool

boolean  false

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GATK version 4.0.9.0 built at 25-11-2019 01:11:10.