To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

baserecalibration without dbSNP file - outcome ?

rnaharrnahar SingaporeMember

Hi

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 ?

Thanks

Best Answer

Answers

  • rnaharrnahar SingaporeMember

    Thanks Sheila for your prompt answer - it helps

Sign In or Register to comment.