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GATKPhaseByTransmission

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

This node is based on the PhaseByTransmission tool of GATK and performs two functions:
1. Computes the most likely genotype combination and phases trios and parent/child pairs given their genotype likelihoods and a mutation prior and
2. Phases all sites were parent/child transmission can be inferred unambiguously.
It reports the genotype combination (and hence phasing) probability.
For further information, see the GATK online documentation of the PhaseByTransmission walker.

Options

PhaseByTransmission

PED File
Set the path to the PED pedigree file containing the description of the individuals relationships.
For further information, see the GATK online documentation on Pedigree/PED files.
De novo prior
Prior probability of de novo mutations. The default value of 1 e-8 is fairly stringent, so if you are interested in maximizing sensitivity at the expense of specificity (i.e. are ok with seeing some false positives as long as all true positives are detected) you will need to relax this value.

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 and select the file in the file browser.
Further options
Set additional command line flags for the GATKPhaseByTransmission.

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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Path to input VCF file

Output Ports

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Cell 0: Path to the phased VCF file

Views

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

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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