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SnpSift

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

This node is a wrapper for the SnpSift toolbox. Various tools allow you to filter and manipulate VCF files (annotated by snpEff).

Options

Select tool
  • Filter: SnpSift filter is one of the most useful SnpSift commands. Using SnpSift filter you can filter VCF files using arbitrary expressions.
  • Annotate: Annotate using fields from another VCF file (e.g. dbSnp, 1000 Genomes projects, ClinVar, ExAC, etc.).
  • TsTv: Calculate the transition to transversion ratios for each sample.
  • Intervals: This tool is used to extract variants that intersect any interval.
  • dbNSFP: The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
  • Other: Use another tool by specifying an individual command.
Individual Command
You can specify an individual command and parameters that are provided by SnpSift, e.g. hwe -q. The output of the specified tool is written into the selected file.

Filter

Filter criteria
Set your filter criteria according to the syntax of SnpSift.

Annotate

VCF file providing annotations
Set a path to a VCF file that provides annotations to be assigned to variants in the input VCF file.
Do not annotate INFO fields
INFO fields are not annotated, i.e. only the ID field is annotated.
List of INFO fields
Annotate using a list of info fields (list is a comma separated list of fields). Default: ALL.
Further annotate flags
Here, you can specify further flags that are supported by the annotate tool.

Intervals

Specify interval file
Select a BED file that defines intervals.
Exclude entries in intervals
If this option is checked, all variants that intersect one of the given intervals will be excluded from the output.

dbNFSP

Specify dbNFSP database
Set the path to the gzipped and indexed dbNFSP.
Include empty values
Annotate fields, even if the database has an empty value (annotates using '.' for empty).
List of field names
A comma separated list of fields to add. Type "java -jar SnpSift.jar dbnfsp" within your terminal to see the full list of default fields.
Further dbnsfp flags
Here, you can specify further flags that are supported by the dbnsfp tool.

Input Ports

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Cell 0: Input VCF file. Some SnpSift tools require files annotated by snpEff.

Output Ports

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Cell 0: The format of the output file depends on the chosen tool.

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)

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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