Quality scores for overlapping paired mates

[elliot-imler]

I'm sure i can figure this out by testing but is there any documentation on how STAR handles the quality scores for merged mapping of overlapping regions on mates, it looks like an intermediate merged single end read is created and used for mapping but there isnt any more detail in the documentation that i can see. dealing with a situation with lower quality reads with overlapping regions that could be used for a useful improving variant calls. ive been using external using tools but i am betting STAR would be much more efficient if i understood how it handles these cases.

[shayanjl]

I am not aware of any clear documentation describing how STAR handles base-quality scores in overlapping mates. So I would avoid assuming STAR performs overlap-aware quality merging in a way that is safe to rely on for variant calling.

If this matters for your pipeline, the safer approach is to handle overlap clipping or merging downstream with dedicated tools, or ask the maintainer directly for the exact behaviour.