stuart

stuart curates SNP genotypes by filtering and formatting SNP marker array genotyping data to support genetic mapping analyses in two-generation crosses.

Key Features:

• Data curation and marker filtering: Curates raw genotyping data from SNP marker arrays by filtering SNPs based on informativeness, Mendelian inheritance patterns, and consistency with parental genotypes.
• R/qtl compatibility: Produces curated datasets formatted for direct compatibility with the R/qtl package for downstream genetic mapping analyses.
• Marker-level quality evaluation: Identifies defective SNP assays and incorrect genotype interpretations at the marker level to improve genotype reliability.

Scientific Applications:

• Genetic mapping in two-generation crosses: Refines genotype datasets used for linkage and QTL mapping in experiments involving two-generation crosses.
• Reduction of spurious results: Mitigates errors arising from defective SNP assays and incorrect genotype calls to increase accuracy of genetic analyses.

Methodology:

Processes raw genotyping data through marker filtering based on informativeness, conformity to Mendelian inheritance patterns, and consistency with parental genotypes, then formats the curated data for compatibility with R/qtl.