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Test-drive the GATK tools and Best Practices pipelines on Terra
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Is the SOR the natural logarithm of odds ratio?
I'm trying to figure out a good threshold for the SOR for hard-filtering a SNP data set. The best practices documentation suggests using a cutoff threshold of 4, but in reading a bit more about odds-ratios, it seems that taking the natural logarithm of the odds-ratio may be more ideal. Is the SOR reported in the vcf file actually the natural logarithm of the odds ratio? This information is not provided in the page on statistical tests or the documentation for the SOR.