“…Exome sequencing studies at moderate (approximately 100X) depth rely on read position to identify potential PCR duplicates [17], but amplicon-based (molecular inversion probes [18], RainDrop Digital PCR (RainDance Technologies, Billerica, MA, USA), TruSeq Custom Amplicon (Illumina, San Diego, CA, USA)) methods commonly used for targeted sequencing have reads with the same start and stop positions. Hybridization-based methods, when sequenced deeply, can result in reads that are not PCR duplicates but have the same start stop locations by chance [19]. PCR-free methods are also available, but typically require higher amounts of DNA input (1 to 2 ug), limiting their use in cancer studies.…”