PBAP

PBAP processes pedigree-based dense genetic marker data to perform quality control, select marker subsets that reduce linkage disequilibrium for linkage analysis, and prepare input files for MORGAN.

Key Features:

• Quality Control: Performs rigorous quality control on pedigree-derived genotype and sequence data to ensure data integrity for downstream analyses.
• Marker Selection: Selects flexible subsets of markers from dense SNP panels and sequence data, including rare variants, to facilitate linkage analysis while reducing computational demands.
• Linkage Disequilibrium Reduction: Minimizes linkage disequilibrium between SNPs through marker subset selection to improve suitability for linkage methods.
• File Preparation for MORGAN: Formats output files specifically for compatibility with MORGAN to support analysis of small and large human pedigrees.
• Support for Sequence Data and Rare Variants: Handles dense marker panels derived from sequence data and incorporates rare variant considerations in marker selection.

Scientific Applications:

• Pedigree-based linkage analysis: Facilitates linkage analysis of human traits by providing QC, LD-aware marker selection, and MORGAN-formatted inputs.
• Small pedigree studies using sequence data: Supports analyses of rare variants and dense marker panels in smaller family-based studies.
• Preprocessing for MORGAN analyses: Supplies preprocessed and formatted datasets ready for downstream analysis with MORGAN on pedigrees of varying sizes.

Methodology:

Computational steps include quality control of genotype and sequence data, selection of marker subsets to minimize linkage disequilibrium for linkage analysis, and formatting of output files for MORGAN.