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SNiPER started as a student project at the Programming For Biology course at Cold Spring Harbor Labs in October 2009. Students who contributed code were (in alphabetical order): Julien Ayroles, Aurelie Bonin, Chris Gregg, Steve Mount, Jen Parla and Ashley Wolf. The group was supported by Jenya (Jean) Babayev, Jan Aerts and the other TAs at the course.


The aim of this project is to build a semi-automated pipeline for the analysis of single-nucleotide polymorphisms (SNPs) based on next-generation sequencing data in human. This pipeline consists of several parts:

  1. Alignment of the original FASTQ files against a reference genome.
  2. SNP calling based on these alignments
  3. Functional annotation for the SNPs (e.g. NON_SYNONYMOUS_CODING, ESSENTIAL_SPLICE_SITE)
  4. Identification of rare/novel SNPs based on comparison with data from 1000 Genomes Project, HapMap and dbSNP.

All data is managed in a relational database.


This github repository is a placeholder until the code from the course has been made available.

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