Package picard.analysis
Class RrbsSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.RrbsSummaryMetrics
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@DocumentedFeature(groupName="Metrics", summary="Metrics") public final class RrbsSummaryMetrics extends MultilevelMetrics
Holds summary statistics from RRBS processing QC
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Field Summary
Fields Modifier and Type Field Description Integer
CPG_BASES_CONVERTED
Number of CpG sites that were converted (TG for +, CA for -)Integer
CPG_BASES_SEEN
Number of CpG sites encounteredDouble
MEAN_CPG_COVERAGE
Mean coverage of CpG sitesInteger
MEDIAN_CPG_COVERAGE
Median coverage of CpG sitesInteger
NON_CPG_BASES
Number of times a non-CpG cytosine was encounteredInteger
NON_CPG_CONVERTED_BASES
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)Double
PCT_CPG_BASES_CONVERTED
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)Double
PCT_NON_CPG_BASES_CONVERTED
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)Integer
READS_ALIGNED
Number of mapped reads processedInteger
READS_IGNORED_MISMATCHES
Number of reads discarded for exceeding the mismatch thresholdInteger
READS_IGNORED_SHORT
Number of reads discarded due to being too shortInteger
READS_WITH_NO_CPG
Number of reads discarded for having no CpG sites-
Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description RrbsSummaryMetrics()
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Field Detail
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READS_ALIGNED
public Integer READS_ALIGNED
Number of mapped reads processed
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NON_CPG_BASES
public Integer NON_CPG_BASES
Number of times a non-CpG cytosine was encountered
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NON_CPG_CONVERTED_BASES
public Integer NON_CPG_CONVERTED_BASES
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
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PCT_NON_CPG_BASES_CONVERTED
public Double PCT_NON_CPG_BASES_CONVERTED
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
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CPG_BASES_SEEN
public Integer CPG_BASES_SEEN
Number of CpG sites encountered
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CPG_BASES_CONVERTED
public Integer CPG_BASES_CONVERTED
Number of CpG sites that were converted (TG for +, CA for -)
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PCT_CPG_BASES_CONVERTED
public Double PCT_CPG_BASES_CONVERTED
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
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MEAN_CPG_COVERAGE
public Double MEAN_CPG_COVERAGE
Mean coverage of CpG sites
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MEDIAN_CPG_COVERAGE
public Integer MEDIAN_CPG_COVERAGE
Median coverage of CpG sites
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READS_WITH_NO_CPG
public Integer READS_WITH_NO_CPG
Number of reads discarded for having no CpG sites
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READS_IGNORED_SHORT
public Integer READS_IGNORED_SHORT
Number of reads discarded due to being too short
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READS_IGNORED_MISMATCHES
public Integer READS_IGNORED_MISMATCHES
Number of reads discarded for exceeding the mismatch threshold
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