picard CollectInsertSizeMetrics

Version:
2.20.x
Identifier: TL_e24fa5_4e.c8

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Overview

This tool provides useful metrics for validating library construction including the insert size distribution and read orientation of paired-end libraries. The expected proportions of these metrics vary depending on the type of library preparation used, resulting from technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing and mate-pair reads, see the GATK Dictionary. The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Note: Metrics labeled as percentages are actually expressed as fractions!

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