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Test-drive the GATK tools and Best Practices pipelines on Terra
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the threshold of variant classification in MuTect
When MuTect performs variant classification in normal data, it distinguished two cases. I understand how to get the prior probability of a non-dbSNP site being a gremline (0.00005) and the prior probability of a dbsnp site being a gremline (0.095). But I do not know how to get the threshold of 2.2 and 5.5 respectively. Can you please show me what is the probability of a site not being a germline variant?
Another question is similar. When performing variant detection in tumor data, what is the probability of a site not being a variant? Thanks for your help!