Galaxy |

CollectWgsMetrics (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

Minimum mapping quality for a read to contribute coverage:

MINIMUM_MAPPING_QUALITY; default=20

Minimum base quality for a base to contribute coverage:

MINIMUM_BASE_QUALITY; default=20

Treat bases with coverage exceeding this value as if they had coverage at this value:

COVERAGE_CAP; default=250

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

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

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/):

MINIMUM_MAPPING_QUALITY=Integer
MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20.

MINIMUM_BASE_QUALITY=Integer
Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20.

COVERAGE_CAP=Integer
CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.
                              Default value: 250.

Additional information

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