title: FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
abstract: 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.
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA and Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: Jianchao
authors.initials: J
authors.lastname: Yao
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA and Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: Kelvin Xi
authors.initials: KX
authors.lastname: Zhang
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA and Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Kramer
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA and Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA and Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
mesh_terms: D019295:Computational Biology; D059472:Exome; D006801:Humans; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion; D012984:Software