Galaxy |

FixMateInformation (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset

Adds the mate CIGAR tag (MC) if true, does not if false:

ADD_MATE_CIGAR; default=True

Assume that the input file is QUERYNAME sorted:

ASSUME_SORTED; default=False

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

Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.

Warning on using ASSUME_SORTED option

Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb is to assume that the BAM you are working with is coordinate sorted.

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 file is queryname sorted, even if the header says
                              otherwise.  Default value: false.

ADD_MATE_CIGAR=Boolean
MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true.

Additional information

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