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Downsample SAM/BAM (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM or BAM dataset

Probability (between 0 and 1) that any given read will be kept:

PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads

Random seed value:

RANDOM_SEED; default=1

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

Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.

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/):

INPUT=File
I=File              The input SAM or BAM file to downsample.  Required.

OUTPUT=File
O=File              The output, downsampled, SAM or BAM file to write.  Required.

RANDOM_SEED=Long
R=Long              Random seed to use if reproducibilty is desired.  Setting to null will cause multiple
                    invocations to produce different results.

PROBABILITY=Double
P=Double            The probability of keeping any individual read, between 0 and 1.

Additional information

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