Welcome to
SNPflow
SNPflow provides an intuitive raw data processing pipeline for large scale genotyping experiments using the TaqMan platform (Applied Biosystems) and/or the Sequenom platform. It automatically merges genotype exports from Applied Biosystems SDS Software 2.2.2 or TyperAnalyzer 4.0., compares the results with a predefined sample list, provides several measures to assess the quality of the genotyping experiment (e.g. call rate, Hardy Weinberg equilibrium or replicate discordance rate), a comparison with HapMap populations and generates a population-wide genotype list ready for the statistical analysis.
The workflow consists of five quick and straight-forward steps:
The upload of the sample list of the genotyped population (Study -> Add).
The upload of the SDS software genotype exports or from TyperAnalyzer 4.0. ZIP files are accepted for populations spanning over several PCR plates (Study -> Process SNP Data).
An editable list of sample names present in the SDS or TyperAnalyzer export files, but not in the sample name list and thus excluded from further processing, e.g. non-template controls (included in 'Process SNP Data').
The definition of the genotype designations for the final export files (included in 'Process SNP Data').
The generation of the final report consisting of a summary including the quality measures and the processed genotypes. The processed genotypes and all reports can be downloaded as Excel files (SNP Report -> Export).