When would an insertion's base be called as N?

[js72587]

I have a couple of occurrences in indel calling where one base in an insertion was called as N (as a made-up but similar example, expected is AGGGTCC but called was AGGGTNC). Could you point me to the code where, or documentation of possible reasons why, this would happen? I tried searching but was unable to find it due to difficulties of searching for mentions of "N". Thanks so much.

[Daniel Cooke]

This can happen if N is present in the input reads - have you looked at the read pileups? You can use the --bamout to get realigned reads.

[js72587]

Thank you!