General: Technical debt: significantly refactor and unify germline and somatic code, remove deprecated code for old versions of tools, optimize WGS performance of read-count collection steps (~25% effort this quarter); Release new versions of germline/somatic CNV/ACNV tools (alpha 1.3); Release alpha version of purity-ploidy tool; Complete automated CNV CRSP evaluation and prioritize development of other automated evaluations (ACNV, WGS, purity/ploidy) based on Cromwell/WDL development and data availability in cloud testing environments [requires help from red team]; Establish baseline performance of tools on cfDNA [requires help from sequencing to provide case and panel-of-normal BAMs]; Establish baseline performance of tools on FFPE [requires help from sequencing to provide case and panel-of-normal BAMs]; Establish baseline performance of tools on tumor-only | GATK CNV: Continue evaluations of new coverage model on germline data and prepare for ExAC run; Write paper for new coverage model | GATK ACNV: Complete TITAN/HCC1143-based evaluation of current version of ACNV and submit paper | Tumor Heterogeneity: Complete evaluation for GATK purity/ploidy tool on simulated and real data | Stretch goals: Investigate improvements for cfDNA pending baseline evaluation; Support transition of modelling FFPE artifacts to CGA; Improve real ground-truth resources for both internal and automated evaluations [requires help from sequencing]; Improve simulated ground-truth resources; Investigate CNV/ACNV improvements: Fourier regularization (will significantly affect detection of common germline CNVs in ExAC), automatic relevance detection, modelling of sample-specific bias, WGS optimization; Begin prototyping of phylogeny tool