Galaxy |

CollectGcBiasMetrics (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset.

Load reference genome from:

Using reference genome:

REFERENCE_SEQUENCE

The size of windows on the genome that are used to bin reads:

WINDOW_SIZE; default=100

For summary metrics, exclude GC windows that include less than this fraction of the genome:

MINIMUM_GENOME_FRACTION; default=0.0005

Calculate the base distribution over PF (passing filtering) reads only:

PF_READS_ONLY

Assume the input file is already sorted:

ASSUME_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

Program to chart the nucleotide distribution per cycle in a SAM or BAM file.

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/):

ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
                              false. Possible values: {true, false}

PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
                              This option can be set to 'null' to clear the default value. Possible values: {true,
                              false}

ASSUME_SORTED=Boolean
AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True

Additional information

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