Class CollectTargetedPcrMetrics


@DocumentedFeature public class CollectTargetedPcrMetrics extends CollectTargetedMetrics<TargetedPcrMetrics,TargetedPcrMetricsCollector>

This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data. It is appropriate for data produced with multiple small-target technologies including exome sequencing an custom amplicon panels such as the Illumina " + TruSeq Custom Amplicon (TSCA) kit.

If a reference sequence is provided, AT/GC dropout metrics will be calculated and the PER_TARGET_COVERAGE option can be used to output GC content and mean coverage information for each target. The AT/GC dropout metrics indicate the degree of inadequate coverage of a particular region based on its AT or GC content. The PER_TARGET_COVERAGE option can be used to output GC content and mean sequence depth information for every target interval.

Note: Metrics labeled as percentages are actually expressed as fractions!

Usage Example

 java -jar picard.jar CollectTargetedPcrMetrics \\
I=input.bam \\
O=output_pcr_metrics.txt \\
R=reference.fasta \\
AMPLICON_INTERVALS=amplicon.interval_list \\
TARGET_INTERVALS=targets.interval_list
Please see the metrics definitions page on TargetedPcrMetrics for detailed explanations of the output metrics produced by this tool.
Collect metric information for target pcr metrics runs. See CollectTargetedMetrics and TargetedPcrMetricsCollector for more information