SNPflow

SNPflow performs quality control and processing of single nucleotide polymorphism (SNP) genotype data from Sequenom iPLEX and ABI 7900HT (TaqMan, KASPar) platforms to enable accurate downstream genetic analyses.

Key Features:

• Automatic Data Processing: Processes raw genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT systems (TaqMan, KASPar) with extensibility for other genotyping methods.
• Quality Control Metrics: Calculates call rate, expected versus real replicate numbers, minor allele frequency (MAF), absolute number of discordant replicates, discordance rate, and performs Hardy-Weinberg equilibrium (HWE) tests.
• Genotype Frequency Comparison: Compares observed genotype frequencies against reference data from HapMap and 1000 Genomes.
• Sex Determination: Determines sample sex from SNP data for DNA quality control and validation.
• Data Storage: Stores processed genotype and QC results in a relational database.

Scientific Applications:

• Large-scale genetic studies: Enables automated QC for studies with extensive SNP datasets and high sample throughput.
• Population genetics: Facilitates assessment of allele frequencies and HWE for population-level analyses.
• Personalized medicine: Supports reliable genotype data generation for genotype-phenotype and clinical association studies.
• Evolutionary biology: Provides validated SNP datasets for analyses of genetic variation and evolutionary inference.

Methodology:

Processes raw genotype files from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar), computes call rate, replicate concordance (expected vs real and absolute discordant counts), discordance rate, minor allele frequency, performs HWE tests, compares genotype frequencies to HapMap and 1000 Genomes, determines sex from SNPs, and stores results in a relational database.