org.broadinstitute.hellbender.tools

Class GatherVcfsCloud

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.GatherVcfsCloud

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
 @BetaFeature
public final class GatherVcfsCloud
extends CommandLineProgram

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
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GatherVcfsCloud.GatherType

Field Summary

Fields

Modifier and Type	Field and Description
int	cloudPrefetchBuffer
boolean	createIndex
boolean	disableContigOrderingCheck
static java.lang.String	GATHER_TYPE_LONG_NAME
GatherVcfsCloud.GatherType	gatherType
static java.lang.String	IGNORE_SAFETY_CHECKS_LONG_NAME
boolean	ignoreSafetyChecks
java.util.List<java.lang.String>	inputs
java.io.File	output

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
GatherVcfsCloud()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	doWork() Do the work after command line has been parsed.

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

IGNORE_SAFETY_CHECKS_LONG_NAME

public static final java.lang.String IGNORE_SAFETY_CHECKS_LONG_NAME

See Also:

Constant Field Values

GATHER_TYPE_LONG_NAME

public static final java.lang.String GATHER_TYPE_LONG_NAME

See Also:

Constant Field Values

inputs

@Argument(fullName="input",
          shortName="I",
          doc="Input VCF file(s).")
public java.util.List<java.lang.String> inputs

output

@Argument(fullName="output",
          shortName="O",
          doc="Output VCF file.")
public java.io.File output

cloudPrefetchBuffer

@Argument(fullName="cloud-prefetch-buffer",
          shortName="CPB",
          doc="Size of the cloud-only prefetch buffer (in MB; 0 to disable).",
          optional=true)
public int cloudPrefetchBuffer

createIndex

@Argument(fullName="create-output-variant-index",
          shortName="OVI",
          doc="If true, create a VCF index when writing a coordinate-sorted VCF file.",
          optional=true)
public boolean createIndex

gatherType

@Argument(fullName="gather-type",
          doc="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.")
public GatherVcfsCloud.GatherType gatherType

ignoreSafetyChecks

@Advanced
 @Argument(fullName="ignore-safety-checks",
          doc="Disable sanity checks to improve performance, may result in silently creating corrupted outputs data")
public boolean ignoreSafetyChecks

disableContigOrderingCheck

@Advanced
 @Argument(fullName="disable-contig-ordering-check",
          doc="Don\'t check relative ordering of contigs when doing a conventional gather")
public boolean disableContigOrderingCheck

Constructor Detail

GatherVcfsCloud

public GatherVcfsCloud()

Method Detail

doWork

protected java.lang.Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.