- Streptococcus pneumoniae
- Genotyping and SNP detection of Streptococcus pneumoniae
- S. pneumoniae Sequence Download Tool
- Francisella tularensis
- Genotyping and SNP detection of Francisella tularensis
- F. tularensis Comparative Analysis Tool
- Haemophilus influenzae
- Genome Sequencing and Species Microarray for H. influenzae
- High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens
- Bioinformatic SNP Filter Scripts
- Poster Presentations
Bioinformatic SNP Filter Scripts
Scripts for Filtering Raw SNP calls from Affymetrix GeneChip® Resequencing Chips
We have developed a set of scripts to identify and remove false positive SNP calls that are present in the CHP files produced by the Affymetrix GSEQ software. These scripts are described in an online presentation available here, and are described more completely in a published manuscript (Nucleic Acids Research 2007; doi: 10.1093/nar/gkm918).
These scripts have been designed to work in our processing environment. The download package includes README files, as well as comments in the individual scripts that should help you adapt them to your environment. However the task of adapting these scripts may not be trivial. We offer these scripts "as-is" in the hopes that they will be useful to some in the research community.
These scripts require the MUMmer sequence alignment tools, which are available for download here. They also make use of the binding energy calculator from the ArrayOligoSelector package (Bozdech et al, http://genomebiology.com/2003/4/2/R9). The source code for the energy calculator is included with our scripts.