SIG Frontiers in Somatic Variant Calling - EMBL 3 Nov 2013

Where: Room B11, ATC building of EMBL Heidelberg
When: Sunday 3 November 2013, 9.00 - 12.00h
Sponsored by the RADIANT project.

While a wealth of groundbreaking science has been achieved, the identification of somatic cancer variants remains challenging, due to clonal heterogeneity, complex structural variants and systematic biases of the technology. A diversity of approaches for controlling false positives or 'artefacts' exist; false negative rates are largely uncontrolled; few systematic benchmarks guide the field. These challenges are becoming more pressing with attempts at integrative "pan-cancer" studies across thousands of samples. The aim of this workshop is to bring together a small set of computational biologists directly involved in designing, benchmarking and applying somatic variant calling, and to exchange technical details and insights that tend to get smoothed over in larger meetings.


9.00WelcomeWolfgang Huber
9.05Competing to find the best mutation callers - DREAM, benchmarks, competition, wisdom-of-crowdsJosh Stuart (UCSC)
9.25Assessing SNV calling in the oesophageal ICGC projectMike Smith (CR UK)
9.37Combining GATK, SAMtools, Varscan2 and pibase for reducing false negatives in somatic SNV-callingMichael Forster (Kiel)
9.50The DKFZ pipeline: somatic SNV calling without statisticsMatthias Schlesner (DKFZ)
10.02Incorporating genome structure into mutation callingMartin Peifer (Cologne)
10.15Subclonal variant calling with multiple samples and prior knowledgeMoritz Gerstung (Sanger)
10.45Towards somatic variant integrationTobias Rausch (EMBL)
10.57Calling somatic events in multiple related tumour samplesMalvina Josephidou (CR UK)
11.10Scalable nucleotide tallies for visualisation and computation on large sets of samplesWolfgang Huber (EMBL)
11.22Discovery and genotyping of twilight zone indelsAlexander Schoenhuth (Amsterdam)
11.35Structural rearrangementsYilong Li (Sanger)

Link to the talks

Wolfgang Huber