Question: Base Recalibration with different dbSNPbuild
0
gravatar for jxk906
2.3 years ago by
jxk9060
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.

Thanks.

dbsnp gatk • 562 views
ADD COMMENTlink modified 2.3 years ago by Kevin Blighe56k • written 2.3 years ago by jxk9060
1
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

Kevin

ADD COMMENTlink written 2.3 years ago by Kevin Blighe56k
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