Base Recalibration with different dbSNPbuild

Question

[jxk906]

Hi, I am trying to clarify whether I can run BaseRecalibration (GATK) 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.

Thanks.

Answer 1

[Kevin Blighe]

I'm not sure that anyone would have done this previously. My own recommendation would to re-analyse the data and then re-perform the BaseRecalibration.

Also, as this is GATK related, you will get a better and more rapid response on the GATK Support Forum

Kevin