Introduction

FamAnn is an automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies. It can apply a different inheritance pattern or a de novo mutations discovery model to each family and select single nucleotide variants and small insertions and deletions segregating in each family or shared by multiple families. It also provides a variety of variant annotations and retains and annotates all transcripts hit by a single variant. Excel-compatible outputs including all annotated variants segregating in each family or shared by multiple families will be provided for users to prioritize variants based on their customized thresholds. A list of genes that harbor the segregating variants will be provided as well for possible pathway/network analyses. FamAnn uses the de facto community standard Variant Call Format as the input format and can be applied to whole exome, genome or targeted resequencing data.https://sites.google.com/site/famannotation/home CONTACT: jianchaoyao@gmail.com, kelvinzhang@mednet.ucla.edu, mccombie@cshl.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
    Cite this
    Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR, 2014-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Jianchao Yao
    Developer

    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, United States of America

  2. Kelvin Xi Zhang
    Developer

    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, United States of America

  3. Melissa Kramer
    Developer

    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, United States of America

  4. Matteo Pellegrini
    Developer

    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, United States of America

  5. W Richard McCombie
    Investigator

    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, United States of America

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Summary
AccessionBT000380
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByW Richard McCombie