This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
questions about how to choose different types of dbSNP files
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.