Purpose

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

Warning on using this tool on BWA-MEM output

This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.

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/):

FILTER=Filter                 Filter.  Required. Possible values:
                              includeAligned [OUTPUT SAM/BAM will contain aligned
                              reads only. (Note that *both* first and
                              second of paired reads must be aligned to be included
                              in the OUTPUT SAM or BAM)],

                              excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
                              (Note that *both* first and second of pair must be aligned to be
                              excluded from the OUTPUT SAM or BAM)]

                              includeReadList [OUTPUT SAM/BAM will contain reads
                              that are supplied in the READ_LIST_FILE file]

                              excludeReadList [OUTPUT bam will contain
                              reads that are *not* supplied in the READ_LIST_FILE file]}

READ_LIST_FILE=File
RLF=File                      Read List File containing reads that will be included or excluded from the OUTPUT SAM or
                              BAM file.  Default value: null.

Additional information

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