Galaxy |

ReorderSam (version 3.1.1.0)

Load reference genome from:

Use dictionary from the list:

Select genome from the list

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset

If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs:

ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False

If true, then permits mapping from a read contig to a new reference contig with the same name but a different length:

ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; 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

ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Not to be confused with SortSam.

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/):

ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference
                              sequence contigs.  By default, this tool requires a corresponding contig in the new
                              reference for each read contig  Default value: false. Possible values: {true, false}

ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same
                              name but a different length.  Highly dangerous, only use if you know what you are doing.
                              Default value: false.  Possible values: {true, false}

Additional information

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