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Collect Alignment Summary Metrics (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset.

Load reference genome from:

Using reference genome:

REFERENCE_SEQUENCE

The level(s) at which to accumulate metrics:

METRIC_ACCUMULATION_LEVEL

Assume the input file is already sorted:

ASSUME_SORTED

Input file contains Bisulphite sequenced reads:

IS_BISULFITE_SEQUENCED

Adapters

Adapter 0

Larger paired end reads and inter-chromosomal pairs considered chimeric:

MAX_INSERT_SIZE

Select validation stringency:

Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

Purpose

Reads a SAM or BAM file and writes a file containing summary alignment metrics.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with
                              inter-chromosomal pairs.  Default value: 100000.

ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may
                              be specified 0 or more times.

METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE,
                              LIBRARY, READ_GROUP} This option may be specified 0 or more times.

IS_BISULFITE_SEQUENCED=Boolean
BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.


REFERENCE_SEQUENCE=File
R=File                        Reference sequence fasta  Default value: null.

ASSUME_SORTED=Boolean
AS=Boolean                    If true (default), then the sort order in the header file will be ignored.

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .