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Is Strand Bias-Fisher's p-value the only p-value we can obtain for a SNP/INDEL call?
Do we have an option to calculate the actual HWE p-value instead of the HWE proportions?
This may be what you're looking for:
Geraldine Van der Auwera, PhD
So does that mean it is not available yet?
I do not see any documentation there! Am I missing something?
No, that means that that's the annotation you need to use (either with one of the callers, or with VariantAnnotator) to get the information you want. If you want more detail as to how this is calculated, that is not currently documented, so you'll need to look at the source code. But presumably if you just want the HW p-value, you can just use the tool.