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roblanf / sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences
GNU General Public License v3.0
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re-root to wh1? #13

Open roblanf opened 4 years ago

roblanf commented 4 years ago

One suggestion from Russ CD is to re-root on WH1, since i use that as a reference for the alignments. This would make mapping mutations more sensible looking.

AngieHinrichs commented 3 years ago

Actually, Wuhan-Hu-1/EPI_ISL_402125/MN908947/NC_045512 (29903 bases) and WIV04/EPI_ISL_402124/MN996528 (29891 bases) are identical except that Wuhan-Hu-1's polyA at the end is 12 bases longer than WIV04's. There is no WIV04 base that differs from Wuhan-Hu-1 (thank goodness). Since the beginning and end of the sequence alignment are masked, there should be no difference between the two sequences as far as phylogeny is concerned, right? So I think this is moot.

AngieHinrichs commented 3 years ago

Sorry, I assumed you were using WIV04|EPI_ISL_402124 because that is GISAID's preferred reference (https://www.gisaid.org/epiflu-applications/hcov-19-reference-sequence/). But I see in global_tree_gisaid.sh it's actually hCoV-19/Wuhan/WH04/2020|EPI_ISL_406801|2020-01-05. That is definitely different (relative to WIV04 or NC_045512 it has 8782 C>T and 28144 T>C).

AngieHinrichs commented 3 years ago

We've been rerooting to Wuhan-Hu-1/NC_045512 for our purposes, so this doesn't directly affect us. I was hoping to give you a reason to simply close this issue, but I was just mixing up WIV04 and WH04, oops.

roblanf commented 3 years ago

Thanks for checking up on that Angie. The trees are about to move to GISAID and be hosted / computed there, so very soon will be a great time for us to revisit this and see what GISAID think is the most sensible place to root the tree!

On Tue, 17 Nov 2020 at 10:48, Angie Hinrichs notifications@github.com wrote:

We've been rerooting to Wuhan-Hu-1/NC_045512 for our purposes, so this doesn't directly affect us. I was hoping to give you a reason to simply close this issue, but I was just mixing up WIV04 and WH04, oops.

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