Question: BQSR using GATK without dbsnp
gravatar for kezcleal
5.4 years ago by
United Kingdom
kezcleal160 wrote:

Hi, I have run the base quality score recalibration (BQSR) tool from GATK but for the known sites parameter I used only two databases:



I realise I should possibly also have included the dbsnp_138 database in this list. Is it necessary to re-run with all three databases?

snp next-gen sequence • 2.4k views
ADD COMMENTlink modified 3.7 years ago by youcai50 • written 5.4 years ago by kezcleal160

Ideally, it would be better if you can re-run the BQSR analysis using both SNPs and Indels. But it may or may not affect the downstream variant results depending on how good your sequencing data is. Honestly speaking, I have never found a big difference in  the number and quality of variants called before or after BQSR but it could be solely due to genuinely good quality of reads that we get from our sequencing core. The other steps such as indelrealignment do have a big effect on the quality of variants.  

ADD REPLYlink written 5.4 years ago by Ashutosh Pandey12k
gravatar for youcai
3.7 years ago by
youcai50 wrote:

I'm working on a genome that doesn't really have a good SNP database yet. I'm wondering if it still makes sense to run base quality score recalibration without known SNPs

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by youcai50
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