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.gzSpecify 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 |
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 | |
--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 ""
--help / -h
display the help message
boolean false
--ignore-safety-checks
Disable sanity checks to improve performance, may result in silently creating corrupted outputs data
boolean false
--input / -I
Input VCF file(s).
R List[String] []
--output / -O
Output VCF file.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--tmp-dir
Temp directory to use.
GATKPath null
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--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
--version
display the version number for this tool
boolean false
GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.
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