SnpSift

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.

Views

STDOUT / STDERR

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

Workflows

• KNIME4NGS_Test_VarCallingKnime4NGS

Links

• No links available

Developers