Question: Base Recalibration with different dbSNPbuild
gravatar for jxk906
2.3 years ago by
jxk9060 wrote:

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.


dbsnp gatk • 562 views
ADD COMMENTlink modified 2.3 years ago by Kevin Blighe56k • written 2.3 years ago by jxk9060
gravatar for Kevin Blighe
2.3 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

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


ADD COMMENTlink written 2.3 years ago by Kevin Blighe56k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1802 users visited in the last hour