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GATKVariantFiltration

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

This node is based on the VariantFiltration tool of GATK which enables hard-filtering variant calls based on certain criteria. Records are hard-filtered by changing the value in the FILTER field to something other than PASS. Use the GATK ExcludeVariants node to remove the filtered variants.
For further information, see the GATK documentation of the VariantFiltration walker.

Options

VariantFiltration

Filter INFO fields
Filter variants according to values of the INFO fields. Variants that match any one of the given conditions will be tagged with 'Filter Name' in the FILTER field. Further conditions can be defined in the 'Additional Filter Options' field. For further information on hard filtering, see howto Apply hard filters to a call set.
Filter FORMAT fields
Filter genotypes according to values of the FORMAT fields. Genotypes that match any one of the given conditions will be tagged with 'Filter Name' in the FT field of the FORMAT fields. Further conditions can be defined in the 'Additional Filter Options' field. If the box is checked, filtered genotypes are set to no-call. Note that allele counts are not recomputed after filtering.

GATK

GATK Memory
Set the maximum Java heap size (in GB).
Path to BED file
Tick this option in order to call variants 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 GATKVariantFiltration.

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 VCF file

Output Ports

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Cell 0: VCF file with adjusted FILTER fields Note that filtered variants can be removed using the GATK ExcludeVariants node.

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)

  • SnpEff (63 %) 
  • GATKExcludeVariants (25 %) 
  • SnpSift (13 %) 

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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