Galaxy |

MergeSamFiles (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset

Merge the sequence dictionaries of the datasets being merged:

MERGE_SEQUENCE_DICTIONARIES; default=False

Assume the input file is already sorted:

ASSUME_SORTED; default=False

Comments

Comment 0

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

Merges multiple SAM/BAM datasets into one.

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/):

ASSUME_SORTED=Boolean
AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output
                              sort order, even if their headers say otherwise.  Default value: false. This option can
                              be set to 'null' to clear the default value. Possible values: {true, false}

MERGE_SEQUENCE_DICTIONARIES=Boolean
MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null'
                              to clear the default value. Possible values: {true, false}

COMMENT=String
CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0
                              or more times.

Additional information

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