Reads mapping
In the first analysis part, reads were mapped using BWA mem software (v0.7.15, Li, 2013) on the Human reference genome (hg19 assembly) using default parameters. As a second quality control, statistics regarding the mapping (percentage of aligned reads total and falling into the capture, percentage of PCR duplicates) and the capture coverage were produced using a combination of SAMtools, flagstat, BEDtools coverage and PicardTools MarkDuplicates.