# About

## About

This project is maintained by [**Pablo Cingolani**](http://www.linkedin.com/in/pablocingolani)

## 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 &amp; 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. <br>
* 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 &amp; 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 &amp;  Eugene Brevdo (SVBio): Insertions in reverse strand bug report and bugfix.
* Uma Devi (U. Virginia), Karen Eilbeck (U. Utah) &amp; Nicole Marie Ruiz (U. Utah): Sequence Ontology, made right.
* Ryan Calhoun (Apistry): SnpSift annotate, tabix index bug.

## Contact information

<strong>[Pablo Cingolani](http://www.linkedin.com/in/pablocingolani).</strong>
