Entering edit mode
9.4 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?
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 indel-realignment do have a big effect on the quality of variants.