Yao, J., Zhang, K. X., Kramer, M., Pellegrini, M., McCombie, W. R. (January 2014) FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. ISSN 1367-4803
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: | 13 January 2014 |
| Date Deposited: | 22 Jan 2014 21:59 |
| Last Modified: | 06 Nov 2015 20:06 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/29343 |
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