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DepthOfCoverage

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

This GATK tool processes an input bam file to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total. The user gets several output tables contain different coverage summaries.
For further information, see GATK documentation of DepthOfCoverage.

Options

Outfile suffix
Define the suffix that will be appended to the outfiles. (Default: Doc)
GATK Filter Terms
Set additional GATK Read Filters that should be used for processing. All Filters can be found in the GATK online documentation.

GATK

GATK Memory
Set the maximum Java heap size (in GB).
Path to BED file
You can check this option to perform the analysis in certain genomic regions. You have to specify the intervals in a text file in BED format (Format explained at http://genome.ucsc.edu/FAQ/FAQformat.html) and select the file in the file browser.
Further options
Set additional command line flags for the DepthOfCoverage.

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to reference sequence
Set the path to the reference reference sequence. This will be done automatically if the path is already defined in the preference page.
Path to GATK jar file
Set the path to GenomeAnalysisTK.jar. This will be done automatically if the path is already defined in the preference page.

Input Ports

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Input BAM file

Output Ports

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Cell 0: File containing per locus coverage

Views

STDOUT / STDERR
The node offers a direct view of its standard out and the standard error of the tool.

Best Friends (Incoming)

Workflows

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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Developers

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