title: Low coverage whole genome seq  from HepG2
design: Shot-gun whole genome libraries  were prepared using the KAPA library preparation kit (KAPA Biosystems). Whole  genome DNA libraries were created, according to manufacturers instructions.  Before end-repair, a 4-hour incubation step at 65C was added to remove as  many reversible crosslinks as possible, after which excessive single stranded  DNA was removed using Mung-Bean nuclease. The concentration of  double-stranded DNA was reassessed using Pico-green and the concentration of  adapters used in the ligation step of the library construction was modified  based on the DNA measured. For the library enrichment, 515 cycles of PCR  with intermediate assessment steps were used instead to ensure low adapter  dimer content and high library yield. Following quantification with qPCR, the  resulting libraries were sequenced on a HiSeq2500 (Illumina) at low coverage  (1) for shallow-seq