Package picard.analysis
Class RrbsSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.RrbsSummaryMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public final class RrbsSummaryMetrics
extends MultilevelMetrics
Holds summary statistics from RRBS processing QC
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Field Summary
FieldsModifier and TypeFieldDescriptionNumber of CpG sites that were converted (TG for +, CA for -)Number of CpG sites encounteredMean coverage of CpG sitesMedian coverage of CpG sitesNumber of times a non-CpG cytosine was encounteredNumber of times a non-CpG cytosine was converted (C->T for +, G->A for -)CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)Number of mapped reads processedNumber of reads discarded for exceeding the mismatch thresholdNumber of reads discarded due to being too shortNumber of reads discarded for having no CpG sitesFields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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READS_ALIGNED
Number of mapped reads processed -
NON_CPG_BASES
Number of times a non-CpG cytosine was encountered -
NON_CPG_CONVERTED_BASES
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -) -
PCT_NON_CPG_BASES_CONVERTED
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction) -
CPG_BASES_SEEN
Number of CpG sites encountered -
CPG_BASES_CONVERTED
Number of CpG sites that were converted (TG for +, CA for -) -
PCT_CPG_BASES_CONVERTED
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction) -
MEAN_CPG_COVERAGE
Mean coverage of CpG sites -
MEDIAN_CPG_COVERAGE
Median coverage of CpG sites -
READS_WITH_NO_CPG
Number of reads discarded for having no CpG sites -
READS_IGNORED_SHORT
Number of reads discarded due to being too short -
READS_IGNORED_MISMATCHES
Number of reads discarded for exceeding the mismatch threshold
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Constructor Details
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RrbsSummaryMetrics
public RrbsSummaryMetrics()
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