Whole-genome fragment libraries were prepared using a modification of Illumina’s genomic DNA sample preparation kit. Briefly, 3 μg of human genomic DNA (Coriell) was sheared for 4 min. on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. The mode of the resulting fragment-size distribution was ~250 bp. End repair, non-templated addition of a 3′-A, adapter ligation and reaction clean-up followed the kit protocol except that we used a generic adapter for libraries destined for shotgun sequencing after hybrid selection. This adapter consisted of oligonucleotides C (5′-TGTAACATCACAGCATCACCGCCATCAGTCxT-3′ with “x” denoting a phosphorothioate bond resistant to excision by 3′-5′ exonucleases) and D (5′-[PHOS]GACTGATGGCGCACTACGACACTACAATGT-3′). The ligation products were cleaned up (Qiagen) and size-selected on a 4% NuSieve 3:1 agarose gel followed by QIAquick gel extraction. A standard prep starting with 3 μg of genomic DNA yielded ~500 ng of size selected material with genomic inserts ranging from ~200 to ~350 bp, i.e., enough for one hybrid selection. To increase the yield we typically amplified an aliquot by 12 cycles of PCR in Phusion High-Fidelity PCR master mix with HF buffer (NEB) using Illumina PCR primers 1.1 and 2.1, or, for libraries with generic adapters, oligonucleotides C and E (5′-ACATTGTAGTGTCGTAGTGCGCCATCAGTCxT-3′) as primers. After QIAquick clean-up, if necessary, fragment libraries were concentrated in a vacuum microfuge to 250 ng per μl before hybrid selection.