SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• High-throughput genotyping technologies generate vast amounts of single nucleotide polymorphism (SNP) data.
• Existing data processing, storage, and quality control methods are time-consuming and require significant bioinformatics expertise.

Purpose of the Study:

• To develop an intuitive and deployable application, SNPflow, to automate and simplify the post-genotyping data analysis pipeline.
• To reduce the time and errors associated with genotype data handling and quality control.

Main Methods:

• SNPflow processes raw genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems.
• The application automates data conversion, calculates quality control metrics (call rate, MAF, discordance, HWE p-value), and compares frequencies to HapMap/1000-Genomes.
• Includes a module for SNP-based sex determination and stores data in a relational database.

Main Results:

• SNPflow successfully automates the conversion of raw genotype data into usable formats.
• Comprehensive quality control metrics are automatically calculated, facilitating data validation.
• The software integrates with population frequency databases for plausibility checks and includes sex determination for quality assurance.

Conclusions:

• SNPflow significantly simplifies and accelerates the post-genotyping analysis workflow for SNP data.
• The application enhances data quality control and accessibility, supporting both stand-alone and laboratory-wide use.
• SNPflow is a valuable tool for researchers working with large-scale SNP genotyping data.