Q: alignment support with supplementary alignments?

[sklages]

When you are implementing alignment support with minimap2[1] will you keep supplementary alignments? At least as an option?
In bonito these alignments are removed and not present in the final BAM file [2].
That's why we are currently separating the basecalling step from the alignment step in our current "bonito workflow"..

[1] lh3/minimap2#1030
[2] nanoporetech/bonito#318

[iiSeymour]

@sklages I'm working through the implementation of this currently so thanks for raising. Yes, I can make supplementary alignments available.

[sklages]

@iiSeymour - I haven't built/tested yet, but does dorado keep supplementary alignments in v0.3.0?

[tijyojwad]

Hi @sklages - yes supplementary alignments should be there in the output. Let us know if you see otherwise

[iiSeymour]

dorado's aligned output matches minimap2 w.r.t sec/sup records and included tags.

[ziphra]

Hi, I think dorado aligned bams miss the SA tag which gives information about supplementary alignments. I used v0.3.1. This is required for some variant callers I believe. At least, sniffles needs it to call translocation.

[tijyojwad]

Hi @ziphra - thank you for highlighting this! SA:Z is indeed missing. We will add it to the next release

[iiSeymour]

@ziphra the SA tag is now present in the v0.3.3 release.