Tuesday, January 7, 2014

Fwd: FamAnn: An Automated Variant Annotation Pipeline to Facilitate Target Discovery for Family-based Sequencing Studies

Fwd: please follow footer link

FamAnn: An Automated Variant Annotation Pipeline to Facilitate Target Discovery for Family-based Sequencing Studies: "

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 (SNVs) and small insertions and deletions (INDELs) 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 which harbor the segregating variants will be provided as well for possible pathway/network analyses. FamAnn uses the de facto community standard Variant Call Format (VCF) 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: Available at Bioinformatics online

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(Via Bioinformatics - Advance Access.)