snpeff.sourceforge.netSnpEff and SnpSift

SnpEff Home Download Documentation SnpSift About SnpEff Home SnpEff description Download Features SnpSift Paper & Citing Who uses SnpEff? Integration Help Bug reports Feature requests Asking for help About Documentation SnpEff manual SnpSift manual Usage Examples SnpEff Genomic variant annotations and functional effect prediction toolbox. Download SnpEff Important: This version implements the VCF annotation standard 'ANN' field . Latest version 4.3T (2017-11-24) Requires Java 1.8 ClinEff Professional verison of SnpEff & SnpSift suites. ClinEff is considered more stable thus suitable for Clinical and Production operations, whereas SnpEff/SnpSfit is designed for Research and Academic usage. Features: Compliance support (CLIA and CAP) Long Term Support Prioritized bug fixes and feature development Customized databases and annotation pipelines Integration with open, private and proprietary databases Privacy: Tickets, issues, pipeline-specific analysis View details » SnpEff Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). Features: Supports over 38,000 genomes . Standard ANN annotation format Cancer variants analysis GATK compatible ( -o gatk ) HGVS notation Sequence Ontology standardized terms View details » SnpSift SnpSift annotates genomic variants using databases, filters, and manipulates genomic annotated variants. Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants for your experiment. View details » Version 4.3 Features: Significant improvements in translocations annotations Improvements in large structural variant annotaions Protein-Protein interaction loci annotations (from PDB) View details » Paper & Citing If you are using SnpEff or SnpSift in an research or academic environment, please cite our papers . View details » Who uses SnpEff? Users of SnpEff include most major research an academic institutions, as well as pharmaceutical companies and clinical sequencing projects. View details » Galaxy, GATK & GKNO SnpEff is integrated with other tools commonly used in sequencing data analysis pipelines. Most notably Galaxy , GATK and GKNO projects support SnpEff. View details » -- In memory of Dr. Xiangyi Lu: Please donate On October 22, 2017, Xiangyi Lu, a co-author on the papers, died of ovarian cancer after a three year struggle. Douglas Ruden, Xiangyi's husband and senior author on the papers, has requested that a non-mandatory gift of at least $10 for using SnpEff or SnpSift be donated to WSU to honor Xiangyi Lu. All gifts will go to a newly named fund, the "Xiangyi Lu Graduate Student Fellowship in Bioinformatics Fund." with the goal of raising $1 million, in order to permanently endow one graduate student research position in bioinformatics every year. -- © Pablo Cingolani...