VCFToolsFilter

The VCFToolsFilter enables to filter VCF files based on VCFTools. Default values are taken from Carson et al. (2014). The output is a VCF file containing the variants that have passed the filters. All INFO fields are included in the output file but values might not be correct due to filtering. However, the node provides the possibility to restore allele counts after filtering.

Options

Further options
VCFTools removes INFO fiels from VCF files. This option enables to restore allele counts (AC).

Genotype Filter

Filter genotype by DP
By setting a threshold for the read depth (DP), genotypes with a DP value below the threshold can be discarded. (Default value = 8)
Make sure that DP values are given in the VCF file!
Filter genotype by AD
Only when using Pindel!
By setting a threshold for the allele depth (AD), genotypes with an AD below the threshold can be discarded. (Default value = 8)
Make sure that AD values are given in the VCF file generated by Pindel!
Filter by GQ
By setting a threshold for the genotype quality (GQ), genotypes with a GQ value below the threshold can be discarded. (Default value = 20)
Make sure that GQ values are annotated in the VCF file!

Variant Filer

Filter by FILTER in PASS
By checking this option variants that have not been assigned to a 'PASS' regarding a previous filter will be discarded.
Filter by call rate
By setting a threshold for the call rate, variants with a call rate below the threshold can be discarded. (Default value = 0.88)
Filter genotypes by mean GQ
By setting a threshold for the genotype quality (GQ), genotypes with a mean GQ value below the threshold can be discarded. (Default value = 35)

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to VCFTool binary
Set the path to vcftools executable. This will be done automatically if the path is already defined in the preference page.

Input Ports

Icon
Cell 0: Path to VCF file

Output Ports

Icon
Cell 0: Path to filtered VCF file

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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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Installation

To use this node in KNIME, install the extension KNIME4NGS from the below update site following our NodePit Product and Node Installation Guide:

v5.9
Plugin provider: IBIS KNIME Team
Plugin version: 1.8.1.201707071203
On NodePit since: 2025-12-11
Last update: 2026-01-10
KNIME versions: Since v3.6

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