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genome / bam-readcount

Count bases in BAM/CRAM files
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Interpretation of indels #104

Closed sakshamphul closed 1 year ago

sakshamphul commented 1 year ago

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

chrisamiller commented 1 year ago

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 1 year ago

C in the question! that helps, thanks!