Dear all
I am trying to use BWA with different penalty score between N mismatch and a base mismatch [ACTG]. Is there any software option that fits my needs?
Let me give you an example:
>Reference
ATTACGTNACT
>Query sequence:: WRT reference it shows 2 changes, first base and the N base
CTTACGTTACT
Using a unique mismatch score, I cannot distinguish the base change C-A and T-N. What I need is a method/option (BWA or other aligners) that assigns a different score to case C-A mismatch (base-mismatch) and T-N mismatch (N-mismatch).
Thank you in advance
Andrea
I am trying to use BWA with different penalty score between N mismatch and a base mismatch [ACTG]. Is there any software option that fits my needs?
Let me give you an example:
>Reference
ATTACGTNACT
>Query sequence:: WRT reference it shows 2 changes, first base and the N base
CTTACGTTACT
Using a unique mismatch score, I cannot distinguish the base change C-A and T-N. What I need is a method/option (BWA or other aligners) that assigns a different score to case C-A mismatch (base-mismatch) and T-N mismatch (N-mismatch).
Thank you in advance
Andrea