In the first part of my talk I will present my view on the state of somatic mutation calling from short reads. I will present results from our effort to experimentally validate somatic mutation calls from 10 different software pipelines on 50 WGS tumour/normal pairs as part of the ICGC/TCGA "Pan-Cancer" project. I will use these results to highlight the strengths of current approaches as well as areas that need further improvement.
In the second part of my talk I will discuss the prospects for using very long sequence reads from nanopore sequencers in cancer genomics. In addition to describing the unique opportunities that nanopore sequencing provides, I will highlight algorithmic and scaling problems that will need to be addressed for this technology to become widely used.