ICGC-TCGA DREAM Genomic Mutation Calling Challenge and forum
- provides bams and fastqs for participants to run variant callers on
- 10 Tumor/Normal matched prostate/pancreatic cancer genomes, 5 from each type, and 5 simulated-sequencing tumors of increasing complexity (a sixth simulated tumor was generated but no truth data has been released for it).
- synthetic tumor data generation, prostate/pancreas real tumor sample preparation
- No ICGC approval is required to access simulated tumour and normal #1, #2, #3 and #6 (as per here)
- So #4 and the faulty dataset (#5) require permission from Here
- BAM access (not tested)
- Truth Data for IS 1-5. Versioned source here
- 6th was released but the VCF truth data is still not available (requests as late as Jan27).
- No reads were uploaded for chromosome 18 "We will modify the evaluations to ignore chromosome 18 for in silico tumour #6 "
- Real Tumor input data is available but truth data not yet released.
ICGC-TCBA SMC (Somatic Mutation Calling) Meta-Challenge
Synopsis: Assuming that different callers take relatively orthogonal methodologies and tend to have independent error profiles, true somatic mutations hopefully gain confidence from most sources, while false positives may be more easily eliminated ... ‘smart’ machine learning-based meta-pipelines are in great need. These meta-pipelines will be independent from the calling algorithms. Information regarding the genomic characteristics, such as GC content, coverage and trinucleotide sequence, can be incorporated.
- Full instructions for contributors
- Input is the union of variant calls for a data set from from Mutation Calling Challenge
- ICGC made GenomicFeatures and SNVCalls files available for each MCC data set. (overview of input data here677, input data available here942).
- Genomic Features calculated described here682
- SNVCalls matrix tells which other callers called each SNV.
- Desired output are (cancer-associated? true-positive?) somatic variant calls.
- Collection of variant calls are the same ones used in the Mutation challenge?