picard.vcf

Class CollectVariantCallingMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.CollectVariantCallingMetrics

public class CollectVariantCallingMetrics
extends CommandLineProgram

Collects summary and per-sample metrics about variant calls in a VCF file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectVariantCallingMetrics.VariantCallingDetailMetrics A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
static class	CollectVariantCallingMetrics.VariantCallingSummaryMetrics A collection of metrics relating to snps and indels within a variant-calling file (VCF).

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	DBSNP
boolean	GVCF_INPUT
java.io.File	INPUT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY
java.io.File	TARGET_INTERVALS
int	THREAD_COUNT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectVariantCallingMetrics()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Option(shortName="I",
        doc="Input vcf file for analysis")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Path (except for the file extension) of output metrics files to write.")
public java.io.File OUTPUT

DBSNP

@Option(doc="Reference dbSNP file in dbSNP or VCF format.")
public java.io.File DBSNP

TARGET_INTERVALS

@Option(shortName="TI",
        doc="Target intervals to restrict analysis to.",
        optional=true)
public java.io.File TARGET_INTERVALS

SEQUENCE_DICTIONARY

@Option(shortName="SD",
        optional=true,
        doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.")
public java.io.File SEQUENCE_DICTIONARY

GVCF_INPUT

@Option(doc="Set to true if running on a single-sample gvcf.",
        optional=true)
public boolean GVCF_INPUT

THREAD_COUNT

@Option
public int THREAD_COUNT

Constructor Detail

CollectVariantCallingMetrics

public CollectVariantCallingMetrics()

Method Detail

main

public static void main(java.lang.String[] args)

doWork

protected int 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:

program exit status.