Hi,
I've thoroughly read the documentation and looked over several examples but want to ensure I am understanding the representation of indels correctly.
Given the following example:
Here are a few statements that I would like some input on. Please let correct these if I'm wrong.
I've thoroughly read the documentation and looked over several examples but want to ensure I am understanding the representation of indels correctly.
Given the following example:
Code:
seq3 200 A 20 ,,,,,..,.-4CACC.-4CACC....,.,,.^~. ==<<<<<<<<<<<::<;2<<
- The 20 suggests 20 total calls (whether reference, alt. ref., or a mismatch) and does not relate to the two deletions (-4CACC) present.
- The corresponding 20 quality values are only for the calls (whether reference, alt. ref. or a mismatch) and do not tell you anything about the deletions.
- The reference call (.) preceding the deletion (-4CACC) is independent of the indel and should be including as a reference allele call similar to the other reference allele calls.