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Simple Example Variant Effect Predictor

Life Sciences Bioinformatics

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This workflow illustrates a simple use of the Variant Effect Predictor verified component. The effect of genetic variants based on their genomic region is determined using Ensembl's Variant Effect Predictor (VEP) via their REST API (https://rest.ensembl.org/#VEP). The output table of the component contains the most severe predicted effect of the variant and the associated gene symbol. In addition, the minor allele frequency from the 1000 genomes project, frequency information from the Genome Aggregation Database (gnomAD), and the SIFT score are extracted (if available). The SIFT Score indicates whether an amino acid substitution affects protein function (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168916/), it ranges from 0 to 1, with low scores indicating a damaging effect. You can also find an application using this component in this blog post https://www.knime.com/blog/variant-prioritization-domain-expert-interaction and here on the KNIME hub: https://kni.me/w/xpPi0YzQ9jwpUC8N

External resources

  • Reproducible Variant Prioritization

Used extensions & nodes

Created with KNIME Analytics Platform version 4.3.0
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    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME REST Client Extension Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME XML-Processing Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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