About - SnpEff & SnpSift
Author: Pablo Cingolani
Description: SnpEff and SnpSift

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# About

This project is maintained by Pablo Cingolani

## Acknowledgements

Acknowledgements and special thanks to (in order of appearance):

- Adrian Platts (McGill): tons of feedback, feature suggestions, test cases, etc.
- Doug Ruden (WSU): feedback, features request, debugging.
- Louis Letourneau (McGill / Genome Quebec): bug fixes, features suggestions, etc.
- Dave OConnor (UW-Madison): feature suggestions, HIV genome.
- Denis Reshetov (Rogaev lab): VCF output support and debugging on GTF parsing.
- Louis Letourneau (McGill / Genome Quebec): Maven project.
- Mark DePristo, Eric Banks & David Rozen (Broad): VCF parsing and VCF output.
- Jonathan Fresnedo (University of California, Davis): P.Persica genome support.
- GATK: integration was performed by Broad's Genome Analysis Team: David Rozen, Eric Banks and Mark DePristo
- Arno Velds (NKI: Netherlands Cancer Institute): Annomalities in ENSEMBL annotation files that led to '-onlyCoding = auto' development, as well as "rogue transcript filters".
- Giulio Genovese: ENSEMBL annotation problems, fixing and improving "rogue transcript" problem.
- Louis Letourneau (McGill / Genome Quebec): dbNSFP implementation
- Peter Briggs (Manchester University) : Improved Galaxy interface and wrappers.
- Jim Johnson (Minnesota Supercomputing Institute, University of Minnesota): SnpSift improvements and bugfixes.
- Davide Cittaro (Center for Translational Genomics and Bioinformatics, Ospedale San Raffaele): Debugging and beta-testing for both SnpEff & SnpSift. Helped to debug many interoperability, compatibility and format specification issues.
- Louis Letourneau (McGill / Genome Quebec): Cancer effects, HSGV notation, etc.
- Sarmady, Mahdi (Children's hospital of Philadelphia): hg19 using transcript version from UCSC.
- Leipzig, Jeremy & Sarmady, Mahdi (Children's hospital of Philadelphia): HGVS notation
- Jinghua (Frank) Feng (University of Adelaide) : Losts of feedback, debugging and improvements in SnpSift annotations.
- Andrea Mafficini (University of Verona, Italy) : Support for dbNSFP 2.1
- Jim Johnson (Minnesota Supercomputing Institute, University of Minnesota): SnpSift 'rmFilter' bugfix.
- Brad Chapman (Harvad): HomeBrew (HomeBrew-Science) support and bash wrapper.
- Marco Cusumano-Towner & Eugene Brevdo (SVBio): Insertions in reverse strand bug report and bugfix.
- Uma Devi (U. Virginia), Karen Eilbeck (U. Utah) & Nicole Marie Ruiz (U. Utah): Sequence Ontology, made right.
- Ryan Calhoun (Apistry): SnpSift annotate, tabix index bug.

## Contact information

Pablo Cingolani.