Due to varying efficiencies of the enrichment baits (e.g., GC / AT content) targeted regions are covered differently and the range and coverage varies over the target region. Eurofins Genomics applies the latest Agilent Human All Exon kit design (V6) with improved design algorithms to better capture hard-to-capture regions providing superior coverage uniformity.
Based on our experience with the sequencing of human samples we typically receive PCR duplicate rates of approximately 5 % for high-quality DNA. If further bioinformatics are ordered (e.g. SNP identification) only one copy of the duplicate read pair is kept in the alignment. The remaining duplicates are excluded from further analysis to prevent bias.