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baserecalibration without dbSNP file - outcome ?
I wanted to know what is expected if one runs the GATK base recalibration without the dbSNP file. From what I understand from the documentation that all sites will be considered for recalibration and no known polymorphic sites will be skipped. This might lower the quality scores at known sites too. Thus one should see a decrease in the number of variants called - am I right ?
I did it by mistake for some of my samples and see an increase in the number of somatic variants called (both tumor and normal were recalibrated without the dbSNP file). Would these extra variants be reliable ?
Any explanations for this ?