picard.analysis

Class CollectWgsMetricsFromSampledSites

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetrics

picard.analysis.CollectWgsMetricsFromSampledSites

public class CollectWgsMetricsFromSampledSites
extends CollectWgsMetrics

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, but only at a set of sampled positions. It is important that the sampled positions be chosen so that they are spread out at least further than a read's length apart; otherwise, you run the risk of double-counting reads in the metrics.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectWgsMetricsFromSampledSites.SampledWgsMetrics

Nested classes/interfaces inherited from class picard.analysis.CollectWgsMetrics

CollectWgsMetrics.WgsMetrics

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INTERVALS

Fields inherited from class picard.analysis.CollectWgsMetrics

COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, REFERENCE_SEQUENCE, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

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

Constructor Summary

Constructors

Constructor and Description
CollectWgsMetricsFromSampledSites()

Method Summary

Modifier and Type	Method and Description
protected CollectWgsMetrics.WgsMetrics	generateWgsMetrics()
protected long	getBasesExcludedBy(picard.analysis.CountingFilter filter) By design we want to count just those bases at the positions we care about, not across the entire read.
protected htsjdk.samtools.util.SamLocusIterator	getLocusIterator(htsjdk.samtools.SamReader in)
static void	main(java.lang.String[] args)

Methods inherited from class picard.analysis.CollectWgsMetrics

doWork

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

INTERVALS

@Option(shortName="INTERVALS",
        doc="An interval list file that contains the locations of the positions to assess.",
        optional=false)
public java.io.File INTERVALS

Constructor Detail

CollectWgsMetricsFromSampledSites

public CollectWgsMetricsFromSampledSites()

Method Detail

main

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

getLocusIterator

protected htsjdk.samtools.util.SamLocusIterator getLocusIterator(htsjdk.samtools.SamReader in)

Overrides:

getLocusIterator in class CollectWgsMetrics

getBasesExcludedBy

protected long getBasesExcludedBy(picard.analysis.CountingFilter filter)

By design we want to count just those bases at the positions we care about, not across the entire read. Therefore, we call filter.getFilteredRecords() so that only the bases in the pileup at a given position are included in the calculations (with filter.getFilteredBases() we would be including other bases in the read too).

Overrides:

getBasesExcludedBy in class CollectWgsMetrics

generateWgsMetrics

protected CollectWgsMetrics.WgsMetrics generateWgsMetrics()

Overrides:

generateWgsMetrics in class CollectWgsMetrics