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param: add XBK to resources and voc
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Katherine Eaton committed Dec 20, 2022
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3 changes: 2 additions & 1 deletion defaults/parameters.yaml
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Expand Up @@ -82,7 +82,7 @@ rule_params:
- delta_omicron: "--clades 21I 21J BA.1 BA.2 --ansi --parents 2-4 --breakpoints 0-10 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3 --ignore-shared --mutation-threshold 0.25"
- omicron_omicron: "--clades BA.1 BA.2 BA.4 BA.5 --ansi --parents 2-4 --breakpoints 0-10 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3 --ignore-shared --mutation-threshold 0.25"
# Current Variants of Concern and Dominant Lineages
- voc: "--clades BA.2.10 BA.2.3.17 BA.2.3.20 BA.2.75 BA.2.76 BA.4.6 BA.5.2 BA.5.3 XBB --ansi --parents 2-4 --breakpoints 1-5 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3 --ignore-shared --mutation-threshold 0.25"
- voc: "--clades BA.2.10 BA.2.3.17 BA.2.3.20 BA.2.75 BA.2.76 BA.4.6 BA.5.2 BA.5.3 XBB CJ.1 --ansi --parents 2-4 --breakpoints 1-5 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3 --ignore-shared --mutation-threshold 0.25"

# ---------------------------------------------------------------------------
# lapis : true if the LAPIS API should be used to query covSPECTRUM to identify the parental lineages.
Expand Down Expand Up @@ -117,6 +117,7 @@ rule_params:
- XAS # Issue #86 | The first parent cannot be differentiated between BA.5 and BA.4 (without using deletions).
- XAV # Issue #104, #195 | Excessive noise/intermissions from conflicting reversions, fails intermission-allele ratio.
- XAZ # Issue #87 | There are no "diagnostic" mutations from the second parent (BA.2).
- XBK # Issue #106 | Breakpoints lie at the extreme 5' end of the genome.

# ---------------------------------------------------------------------------
# extra_cols : (Optional) list of metadata columns to output going forwards (aside from defaults of strain,date,country)
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27 changes: 27 additions & 0 deletions docs/notes/Notes_Development.md
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Expand Up @@ -6,6 +6,33 @@ This is a minor bugfix release aimed towards...

- [Issue #210](https://github.com/ktmeaton/ncov-recombinant/issues/210): Handle numeric strain names.

## Resources

- [Issue #185](https://github.com/ktmeaton/ncov-recombinant/issues/185): Simplify creation of the pango-lineage nomenclature phylogeny to use the [lineage_notes.txt](https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt) file and the [pango_aliasor](https://github.com/corneliusroemer/pango_aliasor) library.

## sc2rf

- [Issue #204](https://github.com/ktmeaton/ncov-recombinant/issues/204): Add special handling for XBB sequenced with ARTIC v4.1 and dropout regions.
- [Issue #205](https://github.com/ktmeaton/ncov-recombinant/issues/205): Add new column `parents_conflict` to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf.
- [Issue #213](https://github.com/ktmeaton/ncov-recombinant/issues/213): Add `XBK` to auto-pass lineages.

- The order of the `postprocessing.py` was rearranged to have more comprehensive details for auto-pass lineages.
- Add `XAN` to auto-pass lineages.

## Plot

- [Issue #209](https://github.com/ktmeaton/ncov-recombinant/issues/209): Restrict the palette for `rbd_level` to the range of `0:12`.

## Validate

### Designated Lineages

- [Issue #196](https://github.com/ktmeaton/ncov-recombinant/issues/196): `XBF`
- [Issue #206](https://github.com/ktmeaton/ncov-recombinant/issues/206): `XBG`
- [Issue #196](https://github.com/ktmeaton/ncov-recombinant/issues/198): `XBH`
- [Issue #199](https://github.com/ktmeaton/ncov-recombinant/issues/199): `XBJ`
- [Issue #213](https://github.com/ktmeaton/ncov-recombinant/issues/213): `XBK`

### Proposed Lineages

- [Issue #203](https://github.com/ktmeaton/ncov-recombinant/issues/203): `proposed1305`
9 changes: 5 additions & 4 deletions resources/breakpoints.tsv
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Expand Up @@ -70,15 +70,16 @@ XAW 895 20056:22577,27875:28310 Delta/21J,Omicron/BA.2/21L,Delta/21J
XBG 896 22600:22916 Omicron/BA.2.76,Omicron/BA.5.2
XAV 911 12161:22791 Omicron/BA.2/21L,Omicron/BA.5.2
proposed1006 1006 26532:27381,27810:29665 Omicron/BA.5/22B,Omicron/BA.2/21L,Omicron/BA.5/22B
XBB 1058 22332:22576 BA.2.10,Omicron/BA.2.75/22D
XBB 1058 22332:22576 Omicron/BA.2.10,Omicron/BA.2.75/22D
XBC 1100 2791:4183,22579:22673,25470:25583 Omicron/BA.2/21L,Delta/21I,Omicron/BA.2/21L,Delta/21I
proposed1138 1138 NA NA
proposed1139 1139 12161:22791 Omicron/BA.2/21L,Omicron/BA.5/22B
XBD 1137 23020:25415 Omicron/BA.2.75/22D,Omicron/BA.5/22B
proposed1229 XBH 15452:22000 BA.2.3.17,Omicron/BA.2.75/22D
XBH 1229 20236:22000 Omicron/BA.2.3.17,Omicron/BA.2.75/22D
XBE 1246 16936:27011 Omicron/BA.5.2,Omicron/BA.5.3
XBF 1259 5184:9865 Omicron/BA.5/22B,Omicron/BA.2.75/22D
proposed1296 1296 5184:12443 Omicron/BA.2.75/22D,Omicron/XBB/22F
proposed1268 1268 23019:23039 Omicron/BA.2/21L,Omicron/BA.5/22B
XBJ 1268 23019:23039 Omicron/BA.2/21L,Omicron/BA.5/22B
proposed1305 1305 27013:27037 Omicron/BA.2.75/22D,Omicron/BA.5.2
XBB_ARTICv4.1 1058 22191:22576 BA.2.10,Omicron/BA.2.75/22D
XBB_ARTICv4.1 1058 22191:22576 Omicron/BA.2.10,Omicron/BA.2.75/22D
XBK 1418 1628:3795 Omicron/BA.5.2,Omicron/CJ.1
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