Snpeff for SV annotation?

[autobot101]

Hello,
It would be helpful to know if Snpeff can annotate structural variants or not, reason being vep is able to annotate, but snpeff always throws some error. Also, does the latest tag on vepgrch38 corresponds to 2.3 version or is it still based on older ones?

Thanks

[maxulysse]

According to snpEff docs, snpEff should only work on SNPs, insertions, deletions and MNPs.

I'm afraid SVs are much more complicated and harder to annotate.

VEP is indeed able to annotate SVs according to docs, but sometimes it throw some errors as well.

I'll make a better filter, so that Manta output are not annotated by snpEff by default.

latest now correspond to 2.3, it shouldn't change much as long as we don't change any Dockerfile.

[autobot101]

Thanks for the info.