File Changes for angie

v424_preview2 to v424_base (2021-11-22 to 2021-12-06) v424

• src/hg/htdocs/images/nextstrain.2021-12-02.png
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    efc54b6ae7a7e9fa7b328fee8aacd47accfb8316 Thu Dec 2 16:45:36 2021 -0800
    Updating track description and colors for addition of Omicron variant.
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
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    8c0b3211b4cb41ba06bff16d0df54b95c9138249 Thu Dec 2 15:39:14 2021 -0800
    Updated B.1.1.529 / Omicron subtracks of VoC track: use Nick's scripts on all available Omicron sequences, thresholds of 0.8 for SNVs, 0.7 for indels.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.html
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    efc54b6ae7a7e9fa7b328fee8aacd47accfb8316 Thu Dec 2 16:45:36 2021 -0800
    Updating track description and colors for addition of Omicron variant.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.ra
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    efc54b6ae7a7e9fa7b328fee8aacd47accfb8316 Thu Dec 2 16:45:36 2021 -0800
    Updating track description and colors for addition of Omicron variant.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    d74f464864e06a125090ce91540e63f46791b4df Mon Nov 29 16:30:48 2021 -0800
    Filter on --max-parsimony after usher run; increase --max-branch-length to 45 to accommodate highly diverged B.1.1.5289/Omicron and add --max-path-length 100 to filter out sequences with a (currently) ridiculous amount of divergence. Annotate Nextstrain clades from nextstrain.clade-mutations.tsv only, no sample-name input. Error out if $prevDate/lineageToName isn't available. Add Pango lineage from tree to Taxonium protobuf output.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    fd84fe49fb0697a08c40b8cdbd1b4b003c06330b Mon Nov 29 12:59:31 2021 -0800
    Now that Problematic Sites track has been updated, no need to patch in masking of site 21987 (S:142).
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    cabd81a0d3b5aecaa7ebc0f7ed86dd541c5330f4 Mon Nov 29 16:13:42 2021 -0800
    Mask deleted bases (and adjacent bases) in the Delta branch to avoid bogus reported SNVs at those locations from erroneous genome assembly pipelines.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    f07eefd7ea1688dfaed14d5860f5663164ecc49c Mon Nov 29 12:55:16 2021 -0800
    Added Nextstrain clades 21I and 21J (Delta sub-clades) and 21K (Omicron). Lots of Ns in 21K path to accommodate sequences with ref-backfilling issues. Also added spaces back to clade names.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    c2fa355ce4dc6f3026a6bfa5a73b910f91c21c45 Wed Nov 17 18:11:38 2021 -0800
    Added AY.122 and renamed AY.12 to AY.122.1 (v1.2.95). Added AY.20.1 and AY.43.{1,2} (v1.2.96). Masked to N bases in regions masked by pangolin but not Problematic Sites (56-265, 29674-29803) so the same file can be used for both full UShER tree and pangolin lineageTree.pb.
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    c53f840e529dc2b335da26189e25059a78d1d712 Mon Nov 29 12:54:18 2021 -0800
    Fixed incorrect path for AY.113. Added new lineages from pango-designation v1.2.98-v1.2.102, including B.1.1.529 (Omicron) for which a lot of sites are N to accommodate sequences with ref-backfilling issues.
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    daffd6b566cb5ba1182be543fe0890c679cce99f Mon Nov 29 15:48:14 2021 -0800
    Added new lineages from pango-designation v1.2.103 (AY.34.1 broadened, new AY.34.1.1 is old AY.34.1).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    d74f464864e06a125090ce91540e63f46791b4df Mon Nov 29 16:30:48 2021 -0800
    Filter on --max-parsimony after usher run; increase --max-branch-length to 45 to accommodate highly diverged B.1.1.5289/Omicron and add --max-path-length 100 to filter out sequences with a (currently) ridiculous amount of divergence. Annotate Nextstrain clades from nextstrain.clade-mutations.tsv only, no sample-name input. Error out if $prevDate/lineageToName isn't available. Add Pango lineage from tree to Taxonium protobuf output.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    4cd889af96dc4c76645d5b3357e47437917bd8e7 Mon Nov 29 15:58:27 2021 -0800
    Make hardcoded path more explicit -- it's my ~/ not just anybody's.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    d1ab093492f89b1fe6130371898d1ac2d47ee85d Mon Nov 29 15:56:05 2021 -0800
    Reroot to lineage A internal node, not leaf sequence. Mask entire untranslated beginning & end of genome like Pangolin does.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    41b65f6c5dd2d79bf2d959abfa8bfa82529d649b Mon Nov 29 15:57:11 2021 -0800
    After completion, grep for signs of trouble when annotating clades & lineages.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
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    76a146dfad5565271b6e29b35ec1ae136fc422aa Mon Nov 29 16:19:01 2021 -0800
    Run and merge 32 usher jobs instead of 16. Don't apply --max-parsimony within usher (too harsh, new highly diverged clusters can't get a foot in the door), leave for post-filtering. Increase para -ram limit. Call maskDelta.sh after merge and before matOptimize. Construct hostfile with only one line per host.