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SamTools

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

The SamTools node enables the access to several SAMtools utilities.
For more information, see the SAMtools help page

Options

Preference page

HTE
Set a threshold for repeated execution.Only used if HTE is enabled in the preference page.
Path to samtools
Set the path to the SAMtools executable (only if no inport is available)
Path to reference sequence
Set the path to the reference sequence (only if no inport is available)

Input Ports

Icon
Optional Inport
Cell 0: Path to input BAM/SAM file

Output Ports

Icon
Cell 0: Path to Outfile

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

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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