GatherVcfsCloud

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

Category Variant Manipulation

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

@author Tim Fennell

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		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. User must have storage.buckets.get permission on the bucket being accessed.
--help -h	false	display the help message
--progress-logger-frequency	10000	The frequency with which the progress is logged to output (i.e. every N records)
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file		A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir		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.

--arguments_file

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

List[File] []

--cloud-prefetch-buffer / -CPB

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

int 2 [ [ -∞ ∞ ] ]

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

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

boolean true

--disable-contig-ordering-check

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

boolean false

--gather-type

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

--gatk-config-file

A configuration file to use with the GATK.

String null

--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 [ [ -∞ ∞ ] ]

--gcs-project-for-requester-pays

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String ""