genome/bam-readcount

Interpretation of indels

sakshamphul opened this issue · 2 comments

sakshamphul commented

alt base is -CT & ref is C. what is alt base ? How do I interpret deletions from bam-readcount?

chrisamiller commented

If I'm interpreting your question properly, at the position indicated by the C, there is a two-base pair deletion of CT (the C in the question, and the following T).

sakshamphul commented

C in the question! that helps, thanks!