FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies

Yao, J., Zhang, K. X., Kramer, M., Pellegrini, M., McCombie, W. R. (2014) FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. ISSN 1367-4803

URL: http://www.ncbi.nlm.nih.gov/pubmed/24395755
DOI: 10.1093/bioinformatics/btt749

Abstract

SUMMARY: 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. AVAILABILITY: 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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > annotation
bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > computers > computer software
Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > McCombie lab
Stanley Institute for Cognitive Genomics
Depositing User: Matt Covey
Date Deposited: 22 Jan 2014 21:59
Last Modified: 06 Nov 2015 20:06
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29343

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