An important issue when creating a pedfile for QC analysis is the choice of strand orientation to use for allele calls (i.e., forward or reverse complement). While forward strand is a commonly used allele coding scheme, Illumina has developed a consistent and simple method to ensure uniformity in genotype call reporting that uses the polymorphism itself and the contextual surrounding sequence (“TOP/BOT” strand and “A/B” allele coding) [18]. Since 2005, the database of genetic variation (dbSNP) [19] has used this designation for all SNP entries. We used “TOP/BOT strand orientation for eMERGE. Choice of strand orientation might depend on the strand orientation of other data used in a combined analysis or of a reference set used for imputation. The goal is to ensure uniformity in genotype call reporting that is critically important in downstream analyses, reporting, and annotation.
