GATKPhaseByTransmission

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.

Views

STDOUT / STDERR

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

Workflows

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Links

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Developers