Data availability

Normal and tumour-paired CRAM files, as well as raw methylation intensity (IDAT) files for the WGS participants from the Sherlock-Lung study, have been deposited in dbGaP under accession numbers phs001697.v2.p1 and phs002992.v1.p1. RNA-seq FASTQ files for the same individuals are available through dbGaP under the accession number phs002346.v1.p1. The human reference genome (GRCh38) was obtained from the GATK resource repository (https://github.com/broadinstitute/gatk/blob/master/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz). Publicly available LUAD multi-omics datasets can be accessed through dbGaP (accessions phs000178.v9.p8 and phs000488.v1.p1) and the European Genome-phenome Archive (EGA) (EGAS00001001757, EGAS00001002801 and EGAS00001003830). Detailed dataset descriptions and accession information are also provided in Supplementary Table 1.

Code availability

The WGS bioinformatics pipelines can be accessed at GitHub (https://github.com/xtmgah/Sherlock-Lung). Battenberg SCNA calling algorithm can be found at GitHub (https://github.com/Wedge-lab/battenberg). The Dirichlet process-based method for the subclonal reconstruction of tumours can be found at GitHub (https://github.com/Wedge-lab/dpclust). The bioinformatic pipeline for identifying TE insertion is available at GitLab (https://gitlab.com/mobilegenomesgroup/TraFiC).

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