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CollectInsertSizeMetrics (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

Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION:

DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0

Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail:

HISTOGRAM_WIDTH; optional

When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads:

MINIMUM_PCT; (Range: 0 to 1). default=0.05.

Assume the input file is already sorted:

ASSUME_SORTED

The level(s) at which to accumulate metrics:

METRIC_ACCUMULATION_LEVEL

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 dataset and writes a file containing metrics about the statistical distribution of insert size (excluding duplicates) and generates a Histogram plot.

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/):

DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
includes enough anomalous values from chimeras and other artifacts to make the mean and
sd grossly misleading regarding the real distribution. Default value: 10.0.

HISTOGRAM_WIDTH=Integer
W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be
included. Default value: not set.

MINIMUM_PCT=Float
M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.

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.

ASSUME_SORTED=Boolean
AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
value: true. This option can be set to 'null' to clear the default value. Possible
values: {true, false}

Additional information

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