questions about how to choose different types of dbSNP files

jingmengjingmeng AustraliaMember

I am pre-processing sequencing exome data according to GATK Best Practice workflows. I have a problem with the process of BQSC (base quality score calibration). According to https://broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php, a dbsnp file needs to be provided. But there are many types of dbsnp, like All.vcf, common_all.vcf, common_and_clinical.vcf. I spend some time understanding these files, but still I do not know which dbsnp file I need to choose to do BQSC. If possible, could you please give me some advice? Thanks very much for your time.

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