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Unanswered Q's

If you have any unanswered questions, please feel free to add them to this list:

Related to the above question, please provide the data or rationale used to justify each of the parameter choices.
Are there any additional parameters or constants beyond those listed in the document? The headings state that these are the “relevant” ones; where can we find the complete list?
What if the top allele is in <50% of reads? What if an insertion or deletion is placed in different positions in a homopolymers run in replicate reads (unlikely but possible even with realignment)?

If you have any unanswered questions, please feel free to add them to this list:

Related to the above question, please provide the data or rationale used to justify each of the parameter choices.
Are there any additional parameters or constants beyond those listed in the document? The headings state that these are the “relevant” ones; where can we find the complete list?
What if the top allele is in <50% of reads? What if an insertion or deletion is placed in different positions in a homopolymers run in replicate reads (unlikely but possible even with realignment)?