Galaxy |

SortSam (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset

Sort order:

SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.

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

Sorts the input SAM or BAM.

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/):

SORT_ORDER=SortOrder
SO=SortOrder          Sort order of output file. You can either sort by queryname or by coordinate.

Additional information

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