WGS of Mus musculus: adult B6CASTF2 male spleen
Genomic DNA was extracted from spleen using the DNAeasy Blood and Tissue Kit (Qiagen), according to the manufacturers instructions. Libraries were prepared by the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (Oxford, UK) using Illumina Nextera DNA Library Prep Kits, with DNA fragmented to an average size of 500 bp. We sequenced to obtain coverage of ~10x for the F0/F4 mice, and ~20x for the F2 and F5 mice via the Illumina Hiseq2500 (F0 and 4 F2 mice; paired 100-bp reads) or Hiseq4000 platforms (remaining mice; paired 100-bp reads for 7 F2 mice, paired 150-bp reads for F4 and F5 mice). Sequencing reads were aligned to mm10 using BWA47 (v. 0.7.0) followed by Stampy48 (v. 1.0.23, option bamkeepgoodreads). We used Picard tools (v. 1.115) (http://broadinstitute.github.io/picard) to merge bam files from different lanes for the same sample and identify duplicate reads.