(2019)1913:67–79.doi:10.1007/978-1-4939-8979-9_5 57. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. (2009) 25:1754–60. doi:10.1093/bioinformatics/btp324 58. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kern ytsky A, et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. (2010) 20:1297–303. doi:10.1101/gr.107524.110 59. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-gen eration DNAsequencingdata. NatGenet. (2011)43:491.doi:10.1038/ng.806 60. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. (2012) 22:568–76. doi:10.1101/gr.129684.111 61. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. (2009) 25:2078–9.doi:10.1093/bioinformatics/btp352 62. LiH.AstatisticalframeworkforSNPcalling,mutationdiscovery ,association mapping and population genetical parameter estimation from sequencing data.Bioinformatics. (2011) 27:2987–93.