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SamtoolsMPileup

Generic Workflow Nodes for KNIME: NgsToolbox version 0.1.0.202003122006 by Freie Universitaet Berlin, Universitaet Tuebingen, and the NgsToolbox Team

samtools mpileup | bcftools -bvcg

Web Documentation for SamtoolsMPileup

Options

per_sample_depth
Per sample read depth.

Input Ports

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Input BAM file. [bam]
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Input Reference file. [fasta,fa,opt.]

Output Ports

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Output BCF file. [bcf]

Views

SamtoolsMPileup Std Output
The text sent to standard out during the execution of SamtoolsMPileup.
SamtoolsMPileup Error Output
The text sent to standard error during the execution of SamtoolsMPileup. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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