Feature request: Compatibility with Starlong

[adbeggs]

Hi

I am trying to do fusion neoantigen prediction using Arriba, however STAR can't cope with long reads and ideally STARlong should be used - do you think this will be able to be supported please?

THanks

Andrew

[suhrig]

To some extent, this is already possible. Technically, Arriba is compatible with STARlong. I just gave it a spin with PacBio long reads and it worked.

The mismappers filter took a very long time to run. It should be disabled for long reads (-f mismappers), since there is a very slim chance of a long read being mapped to the wrong locus anyway.

There weren't any false positives. I am not sure about the false negative rate. Looking at the discarded fusions file, I mainly saw false negatives that were discarded due to lack of support (they had only 1 supporting read). So Arriba reported pretty much everything that can be reported with confidence. So if anything was missed, it was mainly because STAR did not find an alignment. I believe STAR should be able to find most fusions with ease given the long read length. It may have trouble with reads spanning multiple breakpoints (=> unmapped, too short), which may be ameliorated through STAR parameter tweaking. However, STAR will only ever report one chimera per read. Multiple chimeric alignments of the same read are supported by neither STAR nor Arriba.

In addition to disabling the mismappers filter, other Arriba parameters may improve the sensitivity some more. For example, one could reduce the minimum number of supporting reads to 1. I need to give this a try.

What made you think that Arriba is not compatible with STARlong? Did it fail on a sample of yours? Or did it miss fusions in a sample?

[adbeggs]

HI @suhrig - apologies after my post I managed to make it work fine with StarLong - sorry for wasting your time!

[suhrig]

No time wasted. I will make an enhancement that the mismappers filter is skipped for long reads.

If you can share any STAR or Arriba parameter optimizations that improve calling, let me know!