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Base Recalibration with different dbSNPbuild

JaspreetJaspreet Cleveland, OHMember

I wanted to clarify that if I can run BaseRecalibration step using dbSNPbuild 144 on already calibrated bam files with different dbSNP build (138). I am not sure whether it is advisable or will give a drastic change in variation calling? If I could get an insight on this will be really helpful.
Looking forward to your response.


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    I am not sure I understand. Do you want to run BaseRecalibrator on already recalibrated BAM file? Or, do you want to run BaseRecalibrator on original BAM files with a different dbSNP?

    Do not run BaseRecalibrator on already recalibrated BAM files :smiley:

    I am not sure if there will be much of a difference if you use a different version of dbSNP. We have not tested it ourselves and cannot comment. Please let us know of your findings, if there is anything interesting :smile:


  • JaspreetJaspreet Cleveland, OHMember


    Hi Sheila,
    Thank you for your response. Yes, I have already calibrated BAM files (dbSNP138) but wanted to run BaseRecalibrator on these files using dbSNP144 again. I can try using dbSNP144 but as per your post running BaseRecalibrator again on calibrated file is not advisable.

    I don't know whether this question will be appropriate but just wanted to clarify, what could be the possible outcomes using BaseRecalibrator on already calibated BAM files? According to my understanding the calibrated base qualities should not vary. I can be completely wrong but still if you can provide your view will be really helpful.

    Looking forward to your response.


  • JaspreetJaspreet Cleveland, OHMember

    Hi @shlee,

    Thank you for your valuable insight. I'll try it and share the results if something interesting comes up :)

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