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Old 12-31-2010, 06:30 AM   #1
csoong
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Default Quality recalibration on tumor data

Has it occured to anyone that perhaps running GATK recalibration (or any other recal tool) on tumor samples may be problematic?

Because tumor genomes usually have elevated level of mutations, which would be interpreted as unusually high level or errors (mismatches).

What do you think? Any real world experience with this issue?
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