Below are notes from 2013_11_26 telecon between H. Sofia and M. Noble, regarding multi-center mutation calling benchmarks, the file products generated by such, what to do with the latter, and how. The telecon was called to obtain clarity on these, but is not intended to be a definitive policy about any of such.
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Summary
- Since a multi-center MAF is a richer source of data, leading to better science, the ultimate goal should be for them to supplant single-center MAFs
- As of this writing KICH is among the earliest, if not the first, to submit a multi-center MAF to the DCC (through BCM)
- THCA is an example where the multi-center mutation calling benchmark results have not yet been merged back into a single MAF
- There is a seemingly implicit understanding that an analyst or programmer from the primary sequencing center has the responsibility of creating the merged multi-center MAF, by incorporating the calls from secondary centers in the benchmark exercise
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