The custom primer library was designed using the Primer3 algorithm and the manufacturer's suggested parameters (RainDance Technologies Lexington MA, USA). The locations of SNPs in dbSNP build 128 were masked and not used as potential sites for primer selection. Repeat masking was not performed on the input sequences to the primer design pipeline. The primer design pipeline performed exhaustive primer selection across the targeted intervals. Targeted regions that failed to produce PCR primers with the standard parameters through the automated pipeline were designed manually, altering different standard parameters until a successful design was achieved (Table S2 in Additional file 2). After designing the locus-specific portion of the primers, sequence tails corresponding to a portion of the Illumina adaptor sequence were added to the sequence-specific portion of the primers prior to synthesis. The sequence added to the forward primers was CGCTCTTCCGATCTCTG and the sequence added to the reverse primer was CGCTCTTCCGATCTGAC. The tri-nucleotide sequence in bold is inserted between the target specific and the universal primer to confer adapter-strand specificity so that only the reads originating from the same end of
