Replace N's with the reference

[migrau]

Hi,
For very bad alignments with a lot of gaps, is it possible to fill them using the reference instead N's?
Thanks!

[bede]

Hi : ) Could you be more specific about what you mean by 'the' reference?

[migrau]

hi bede! E.g.

Ref.       AATGTCGGCT
read1    TAT
read2    TAT
read3                   GACT
read4                   GACT
kindel:    TATNNNGACT
desired: TATGTCGACT

Another question I just thought about, what is the kindel result if read1 is TCT and read2 TGT? So in the second position we would have A (ref), C (read1) and G (read2). It chooses the ref value for the 2nd postion (A)?

Thanks!

[bede]

Thanks for clarifying Miquel. At the moment this tool infers consensus using the SAM/BAM alone, meaning that to do this I would either have to rely on the SAM/BAM MD string for mismatching positions, which isn't generated by all aligners, or else accept a reference sequence as an optional argument. I did explore the former in a previous version of kindel, but for one reason or another moved away from this approach.

I agree that this would be a useful feature, and will see if I can find time to implement it. In the meantime if you find another tool that performs this task, please do let me know : )

Leaving this issue open.