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Update default mask parameters to mask 200 bases from the end of the genome rather than the existing 50. This was necessary because there is a large deletion in this region in circulating 21L viruses. This deletion is causing problems with alignment and the resulting mis-alignment appears as excess mutations in the tree.
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Worth noting that if/when Nextalign can handle this deletion better, this masking could be reduced. |
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Description of proposed changes
Update default mask parameters to mask 200 bases from the end of the genome rather than the existing 50. This was necessary because there is a large deletion in this region in circulating 21L viruses. This deletion is causing problems with alignment and the resulting mis-alignment appears as excess mutations in the tree.
The issue can be currently seen at https://nextstrain.org/ncov/gisaid/global?c=gt-nuc_29765,29766,29767,29768,29760&m=div.
Testing
Testing has been fairly extensive with @corneliusroemer's https://nextstrain.org/groups/neherlab builds using https://github.com/neherlab/ncov-simple.
Release checklist
docs/src/reference/change_log.mdin this pull request to document these changes by the date they were added.