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Picard Collect Sequencing Artifact Metrics (version 3.1.1.0)

SAM/BAM Input file:

Load reference genome from:

Use dictionary from the list:

Select genome from the list

How many nucleotides (context) on each side to consider:

e.g NXN corresponds to 1 "N" on each side of "X"

Contexts to print in the detailed tables, separated by comma (avoid spaces):

e.g. (for context size=1) AAA,AGG. Default prints all contexts

Minimum base quality score:

Maximum insert size:

Minimum insert size:

Minimum mapping quality:

Assume SAM/BAM is sorted:

Include duplicates:

Include unpaired reads:

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 distribution of potential sequencing "single nucleotide mutation" artifacts 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/):

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

CONTEXT_SIZE=integer            The number of context bases to include on each side of the assayed base.

CONTEXT_SIZE_TO_PRINT=String    If specified, only print results for these contexts in the detail metrics output.
                                However, the summary metrics output will still take all contexts into consideration.

DB_SNP=text file                VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.

INCLUDE_DUPLICATES=Boolean      Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.

INCLUDE_UNPAIRED=Boolean        Include unpaired reads. If set to true then all paired reads will be included as well -
                                MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.

MAXIMUM_INSERT_SIZE=Integer     The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
                                Default = 600

MINIMUM_INSERT_SIZE=Integer     The minimum insert size for a read to be included in analysis. Default = 60

MINIMUM_MAPPING_QUALITY         The minimum mapping quality score for a base to be included in analysis. Default = 30

MINIMUM_QUALITY_SCORE           The minimum base quality score for a base to be included in analysis. Default = 20

Additional information

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