picard

picard CollectAlignmentSummaryMetrics

picard CollectAlignmentSummaryMetrics

Version:
2.20.x
Identifier: TL_e24fa5_40.c8
Tool

Description


Produces a summary of alignment metrics from a SAM or BAM file. This tool takes a SAM/BAM file input and produces metrics detailing the quality of the read alignments as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters. Note that these quality filters are specific to Illumina data; for additional information, please see the corresponding GATK Dictionary entry. Note: Metrics labeled as percentages are actually expressed as fractions!

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