Method for distinguishing PCR-induced errors from sequencing errors

[dnbaker]

For families of reads where the consensus base does not match our reference, we should check to see what fraction of the reads supported that incorrect base. I expect to see errors scattered throughout the reads, but only piling up in PCR or other chemistry-related events.

This will also get us a clearer/better idea as to how effective BMFTools is at eliminating sequencing errors by separating chemical from optical errors.

[dnbaker]

We might get around to this at some point, but juice is likely not worth the squeeze.