BQSR using GATK without dbsnp
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6.9 years ago
kezcleal ▴ 160

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

Mills_and_1000g_gold_standard_indels

1000G_phase1.indels 

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?

sequence next-gen snp • 3.3k views
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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.  

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