Using FunSeq2 for Coding and Non‐Coding Variant Annotation and Prioritization

Priyanka Dhingra1, Yao Fu2, Mark Gerstein3, Ekta Khurana4

1 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10021, 2 Bina Technologies, Roche Sequencing, Redwood City, California, 3 Department of Computer Science, Yale University, New Haven, Connecticut, 4 Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 15.11
DOI:  10.1002/cpbi.23
Online Posting Date:  May, 2017
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The identification of non‐coding drivers remains a challenge and bottleneck for the use of whole‐genome sequencing in the clinic. FunSeq2 is a computational tool for annotation and prioritization of somatic mutations in coding and non‐coding regions. It integrates a data context made from large‐scale genomic datasets and uses a high‐throughput variant prioritization pipeline. This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user‐defined annotations, and (c) detect differential gene expression. © 2017 by John Wiley & Sons, Inc.

Keywords: disease‐causing; differential gene expression; cancer drivers; indels; non‐coding variants; single nucleotide variants

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Table of Contents

  • Introduction
  • Basic Protocol 1: Using FunSeq2 Variant Annotation and Prioritization Via the Web Interface
  • Basic Protocol 2: Using the Command‐Line LINUX/MAC OS Compatible Version of FunSeq2 for Variant Annotation and Prioritization
  • Basic Protocol 3: FunSeq2 for Detection of Differentially Expressed Genes
  • Support Protocol 1: Running FunSeq2 with User Data Context
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
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