beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers
Imports bead-summary data from Illumina scanner.
Pre-processes using a suite of optional normalizations and
transformations. Clusters and automatically calls genotypes,
critically able to handle markers in duplicated regions of the
genome (multisite variants; MSVs). Interactive clustering if
needed. MSVs with variation in both paralogs may be resolved
and mapped to their respective chromosomes. Quality control
including pedigree checking and visual assessment of clusters.
Too large data-sets are handled by working on smaller subsets
of the data in sequence.