Purpose

Computes a number of metrics that are useful for evaluating coverage and performance of datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Obtaining bait and target interval files in Picard interval_list format

This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format. You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries for sequencing, which can generally be obtained from the kit manufacturer. If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format using Picard's BedToIntervalList tool, which will also add the required SAM style header.

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: 200.
CLIP_OVERLAPPING_READS=Boolean
                              If true, clip overlapping reads, false otherwise. Default value: true.

Additional information

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