Description of the lane-level processing of our analysis pipeline. (a-d) The issues that our lane-level processing addresses. (a) Insert length-related complications. (b) The various ways a pair of reads can align, with 1) showing a proper-pair alignment. (c) How PCR duplicates look after alignment. (d) A cartoon of off-target reads and off-target bases of on-target reads. (e) The steps we take to address the issues demonstrated in (a-d). See the Materials and methods section for detailed descriptions.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97