Anne-Katrin Emde, Tobias Rausch, Stefan Haas, and Knut Reinert


SnpStore is a program for SNP and indel calling in mapped next-generation sequencing read data. It features a simple threshold-based model for SNP and indel calling, and a MAQ-like Bayesian model for SNP genotype calling. Reads can optionally be realigned, using the ReAligner algorithm by Anson and Myers.

Main Features

  • threshold-based indel and SNP detection
  • probability-based SNP genotype calling using quality values
  • realignment of reads for improved indel detection
  • import of mapped reads in GFF file (SAM import coming soon)
  • import of reference sequence in Fasta file

SnpStore Binaries

Precompiled binaries are available for 32bit Windows and 64bit Linux.
Alternatively, SnpStore can be obtained as part of the SeqAn library and built locally, see SeqAn Getting Started guidelines. For usage instructions, please take a look at the README file in the downloadable zip-file.

Version History

2011-04-27: v1.0

  • first release of SnpStore


For questions, comments, or suggestions feel free to contact Anne-Katrin Emde.

Last Update 17. September 2012