Also commit clade-defining SNPs?

[biocyberman]

Hi @aineniamh
Could you also commit the clade defining SNPs output (defining_snps.csv) ? That will be helpful to see how each clade is defined at the sequence level. Besides regenerating from the alignment of representative sequences may introduce some discrepancies.

[aineniamh]

HI @biocyberman, yes will do that. I'm starting to prepare the next data release and will make sure that's a part of the information in it.

[biocyberman]

Would it be several days or more until the next release of data? In that case, it will be great if you could publish the defining snps for the current release (if you still have it).

[aineniamh]

I'm doing it now, should be ready by tomorrow if that's soon enough. I think it's worth waiting for the new release as there are a couple of lineages flagged for removal.

[biocyberman]

Perfect! I will wait.

[aineniamh]

Hi @biocyberman, I've published the latest release. It took longer than expected, however am still sorting out some kinks in the lineage defining SNP assignment.

We're finding that (potentially due to homoplasies) there are still a couple of lineages without lineage defining SNPs being called, despite a branch with good support for the lineage existing. I'm fixing this as a priority, but wanted to get the new release out as soon as I could. I'll let you know when it's been fixed, thanks again for your patience.

[biocyberman]

Really appreciate your effort @aineniamh

[rainwala]

Hello all, is this issue still being worked on? It's been a while since the last comment so I'm not sure. If it's available, if you could please point me to the lineage-defining SNP file? Thank you.