MouseDivGeno

MouseDivGeno performs genotype calling and Variable INtensity Oligonucleotide (VINO) probe identification on Mouse Diversity Genotyping Array (Affymetrix; analogous to human SNP 6.0) data to improve genotype accuracy and reduce SNP ascertainment bias.

Key Features:

• Genotype Calling: Converts hybridization intensities from allele-specific oligonucleotide probes into genotype calls using advanced clustering algorithms.
• VINO Identification: Detects probe sets with reproducible atypical hybridization intensity patterns (VINOs) that represent variants not accounted for in array design and recovers data otherwise discarded.
• Copy Number Variation (CNV) Analysis: Provides functionalities to perform CNV analysis on high-density genotyping array data.
• Cross-platform VINO Detection: Recognizes atypical hybridization patterns across genotyping platforms including arrays developed for humans, dogs, cattle, and mice.

Scientific Applications:

• Improved Genotype Accuracy: Incorporating VINOs into analyses increases the accuracy of genotype calls derived from Mouse Diversity Genotyping Array data.
• Reduction of Ascertainment Bias: Identification and use of VINOs mitigates SNP ascertainment bias by recovering miscalled or uncalled genotypes.
• Phylogenetic and Haplotype Analysis: Inclusion of VINOs improves species-tree inference and local haplotype assignment, as demonstrated in Mus species tree construction and laboratory mouse strain analysis.

Methodology:

Converts hybridization intensities to genotype calls using clustering algorithms; identifies VINOs by detecting reproducible atypical hybridization intensity patterns across allele-specific oligonucleotide probes on high-density genotyping arrays (Mouse Diversity Genotyping Array, Affymetrix) and supports CNV analysis and cross-platform VINO recognition.