Class CollectHsMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.directed.CollectTargetedMetrics<HsMetrics,HsMetricCollector>
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- picard.analysis.directed.CollectHsMetrics
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@DocumentedFeature public class CollectHsMetrics extends CollectTargetedMetrics<HsMetrics,HsMetricCollector>
This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing; for more information, please see the corresponding GATK Dictionary entry.
This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format. You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries for sequencing, which can generally be obtained from the kit manufacturer. If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format using Picard's BedToInterval tool.
If a reference sequence is provided, this program will calculate both AT_DROPOUT and GC_DROPOUT metrics. Dropout metrics are an attempt to measure the reduced representation of reads, in regions that deviate from 50% G/C content. This reduction in the number of aligned reads is due to the increased numbers of errors associated with sequencing regions with excessive or deficient numbers of G/C bases, ultimately leading to poor mapping efficiencies and low coverage in the affected regions.
If you are interested in getting G/C content and mean sequence depth information for every target interval, use the PER_TARGET_COVERAGE option.
Note: Metrics labeled as percentages are actually expressed as fractions!
Usage Example:
java -jar picard.jar CollectHsMetrics \\
I=input_reds.bam \\
O=output_hs_metrics.txt \\
" R=reference.fasta \\
BAIT_INTERVALS=bait.interval_list \\
TARGET_INTERVALS=target.interval_listPlease see CollectHsMetrics for detailed descriptions of the output metrics produced by this tool.
SeeHsMetricCollector
andCollectTargetedMetrics
for more details.
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Field Summary
Fields Modifier and Type Field Description List<File>
BAIT_INTERVALS
String
BAIT_SET_NAME
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Fields inherited from class picard.analysis.directed.CollectTargetedMetrics
ALLELE_FRACTION, CLIP_OVERLAPPING_READS, COVERAGE_CAP, INCLUDE_INDELS, INPUT, METRIC_ACCUMULATION_LEVEL, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, TARGET_INTERVALS, THEORETICAL_SENSITIVITY_OUTPUT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectHsMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected htsjdk.samtools.util.IntervalList
getProbeIntervals()
protected String
getProbeSetName()
protected HsMetricCollector
makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance)
A factory method for the TargetMetricsCollector to use this time.-
Methods inherited from class picard.analysis.directed.CollectTargetedMetrics
customCommandLineValidation, doWork
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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BAIT_INTERVALS
@Argument(shortName="BI", doc="An interval list file that contains the locations of the baits used.", minElements=1) public List<File> BAIT_INTERVALS
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BAIT_SET_NAME
@Argument(shortName="N", doc="Bait set name. If not provided it is inferred from the filename of the bait intervals.", optional=true) public String BAIT_SET_NAME
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Method Detail
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getProbeIntervals
protected htsjdk.samtools.util.IntervalList getProbeIntervals()
- Specified by:
getProbeIntervals
in classCollectTargetedMetrics<HsMetrics,HsMetricCollector>
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getProbeSetName
protected String getProbeSetName()
- Specified by:
getProbeSetName
in classCollectTargetedMetrics<HsMetrics,HsMetricCollector>
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makeCollector
protected HsMetricCollector makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance)
Description copied from class:CollectTargetedMetrics
A factory method for the TargetMetricsCollector to use this time. Examples of TargetMetricsCollector: (TargetedPcrMetricsCollector, HsMetricsCalculator)- Specified by:
makeCollector
in classCollectTargetedMetrics<HsMetrics,HsMetricCollector>
- Returns:
- A TargetMetricsCollector to which we will pass SAMRecords
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