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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.