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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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When would an insertion's base be called as N? #234

Closed js72587 closed 2 years ago

js72587 commented 2 years ago

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.

dancooke commented 2 years ago

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 commented 2 years ago

Thank you!