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pastvir channing-zeng hsnguyen banijolly donalbonny angiehinrichs carlacummins rdeborja emilymmaier l-bevc v-julia stevencholland poonlab jpalmer37 artpoon miseminger

constellations's Issues

Add remaining WHO VOI definitions

Add WHO VOI definitions for Iota (B.1.526) and Epsilon (B.1.427/429)

Include all mutations in definition files?

At the moment it is inconsistent whether the definition files contain all mutations from reference or just the ones on the stem branch. I.e., P323L, D614G etc. For simplicity and consistency, it may be good to include all of them. But the required number of 'alts' would need to be revised up.

Comments in site definitions are problemaic

Lines like this (BY.2-like definition):

        "nuc:T22200G # spike:V231G # but this seems to be wrong aa ref allele",

brake all automated parsing of these json files. Perhaps a dedicated comment tag is needed. This has very bad implications for anyone who automates definition retreaval.

cB.1.617.1.json causing error

cB.1.617.1.json cannot be read by the JSON parser

cB.1.526.json too narrow: excludes 66 of 253 representative sequences in pango-designation for B.1.526 / Iota

Iota / Nextstrain 21F / B.1.526 (excluding the former B.1.526.1 which was just redesignated as B.1.637 in cov-lineages/pango-designation#154) is split into two major branches. One (the original B.1.526 from Feb. 2021) has S:E484K (and S:A701V, N:P199L, N:M234I); the other (formerly B.1.526.2 from Mar.-Jun. 2021, then folded into B.1.526) has S:S477N (and S:Q957R, N:P13L, N:S202R).

With the change in pangolin v3.1.9 to remove VoC calls from pangoLEARN/usher that were not supported by scorpio, many USA sequences formerly assigned B.1.526 were reassigned to 'None' because scorpio did not detect them as cB.1.526. I believe this is because those sequences belong to the second branch, while cB.1.526.json has mutations that favor the first branch and not the second.

I ran scorpio classify on aligned fasta for the 253 representative B.1.526 sequences in pango-designation/lineages.csv with the options that pangolin uses (but only with cB.1.526.json):

scorpio classify \
    -i B.1.526.reps.aligned.fa \
    -o B.1.526.reps.scorpio.report.txt \
    --output-counts \
    --constellations constellations/definitions/cB.1.526.json \
    --pangolin \
    --list-incompatible \
    --long &> B.1.526.reps.scorpio.log

grep True B.1.526.reps.scorpio.report.txt.Iota__B.1.526-like__counts.csv | wc -l
187

grep False B.1.526.reps.scorpio.report.txt.Iota__B.1.526-like__counts.csv | wc -l
66

grep False B.1.526.reps.scorpio.report.txt.Iota__B.1.526-like__counts.csv | head
USA/CT-Yale-2729/2021,4,15,0,0,1,0.789500,0.210500,False
USA/CT-Yale-2727/2021,4,15,0,0,1,0.789500,0.210500,False
USA/CT-Yale-2726/2021,4,15,0,0,1,0.789500,0.210500,False

B.1.526.reps.scorpio.report.txt.Iota__B.1.526-like__counts.csv

187 of the 253 representative sequences were identified as cB.1.526/Iota as expected, but 66 were not. Of the 66, all had sufficient alternate alleles (15; min_alt is 11) but one too many reference alleles for cB.1.526.json (4; max_ref is 3).

I think a reasonable way to fix this would be to add mutations to cB.1.526.json that represent the S:477N branch, and increase max_ref accordingly (perhaps also min_alt? but I'm not sure how that's usually determined). I will make a pull request for your consideration.

Define minimal required scorpio version

@aineniamh just having experienced cov-lineages/pangolin#445, what do you think about adding a
__min_scorpio_version__ to constellations' __init__.py?
This would be a more straightforward place to check than the release notes.
I would also be willing to work on adding a corresponding compatibility check to pangolin to warn users about potential issues.

Accommodate WHO VOC/VOI labels in definition files.

Suggest using the label Alpha (B.1.1.7-like) in Scorpio.

Check sensitivity of current definition rules

The calling rules are currently max_ref=3 and min_alt=max(N-8, 5) where N is the number of defining muts.

Combining constellations with type_variant

Our team is trying to create a table of mutations (rows = samples, columns = mutations, cell value = alleles), specifically those mutations which define variants / lineages of concern (e.g. those included in the scorpio's constellation definitions).

Our plan is to use type_variants.

Instead of defining and maintaining a config.csv for type_variant, we were planning to parse the json files in scorpio's constellation definitions) to extract the sites fields a make a list of unique mutations to be used as config.csv.

I guess comments / requests / issues are:

Do you plan to include such feature in pangolin, scorpio or type_variant?
nucleotide changes in scorpio's constellation definitions begin with nuc: while type_variant expects snp:
amino acid changes in scorpio's constellation definitions begin with gene name while type_variant expects aa:
We found some lower / upper case variability in S gene (see #17)

Thanks in advance and congratulations on the great set of tools!

`nuc:C15714T` appears twice in definition of cBA.2

The nucleotide mutation C15714T appears twice in the cBA.2 pango lineage which is one of the Omicron lineages

https://github.com/cov-lineages/constellations/blob/main/constellations/definitions/cBA.2.json

(I am using the constellation definitions to create synthetic reads for testing a bioinformatics pipeline and this borked my code as it had already done the mutation).

Create definition file for B.1.621

cov-lineages/pango-designation#57

Central American? lineage with Spike N501Y, E484K, R346K, and P681H

Constellation for B.1.1.7

I think coordinate for 3 synonymous sites from cB.1.1.7.json are not correct, they're 0-based instead of 1-based:

nuc:C912T
nuc:C16175T
nuc:T2680C

This resulted in scorpio call always have 3 ref alleles using this constellation file. Can you please check @rambaut ?
Thanks.

warnings/errors when using certain json with scorpio

found these warnings when using the various .json files with scorpio:

Parsing constellation JSON file ./constellations/constellations/definitions/cA.23.1+E484K.json
variants file says reference amino acid in CDS orf1a at position 741 is L, but reference sequence has F

Parsing constellation JSON file ./constellations/constellations/definitions/cB.1.1.318.json
variants file says reference amino acid in CDS orf1a at position 1693 is K, but reference sequence has P

Parsing constellation JSON file ./constellations/constellations/definitions/cB.1.324.1.json
variants file says reference amino acid in CDS orf1a at position 76 is G, but reference sequence has A

Parsing constellation JSON file ./constellations/constellations/definitions/cB.1.525.json
variants file says reference amino acid in CDS orf1a at position 323 is P, but reference sequence has C

Parsing constellation JSON file ./constellations/constellations/definitions/cB.1.617.1.json
variants file says reference amino acid in CDS orf1a at position 77 is T, but reference sequence has R

Parsing constellation JSON file ./constellations/constellations/definitions/cB.1.617.3.json
variants file says reference amino acid in CDS orf1a at position 1526 is A, but reference sequence has E

Parsing constellation JSON file ./constellations/constellations/definitions/cP.3.json
variants file says reference amino acid in CDS orf1a at position 736 is D, but reference sequence has P

Compatibility definition for v0.1.11 in pangolin

Following the update to v0.1.11 for constellations

#66

I installed a clean version of pangolin including the following line in the .yaml:

- pip
       https://github.com/cov-lineages/constellations/archive/refs/tags/v0.1.11.tar.gz

When verifying via pangolin --all-versions
version v0.1.10 is listed

Does https://github.com/cov-lineages/pangolin/blob/master/pangolin/data/data_compatibility.csv
need a line entry for constellations 0.1.11?

and do you think that, when installed via yaml rather than pangolin --update, I am seeing a faulty notice for a true 0.1.11, or that the install did enforce an older version of constellations due to either my pip pointer or the pangolin logs?

Question: Nucleotide mutations behind amino acid mutations in .json definitions

Hello,

For every constellation, a definition file is present in definitions/,
Mutations are written in different ways: nucleotide and amino-acid. However, for amino-acid mutations, multiple nucleotide mutations in a codon can result in the same resulting amino-acid.
Do you have an underlying list of nucleotide mutations behind these amino-acid mutations?
If not, what is the rationale behind this seeming "loss of information"? Does only the resulting functional gene matter for virus behaviour and is it therefore not of importance which nucleotide is mutated?

Thank you in advance,
and kind regards,
Michaël

Error in decoding cB.1.617.1.json

When running scorpio I get the following error. I found that the related JSON file has been already fixed in commit ac56ab5. Would you mind to put out a new release so that pangolin can update the definitions?

Thanks for your work

Traceback (most recent call last):
  File "/opt/conda/envs/pangolin/bin/scorpio", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/scorpio/__main__.py", line 220, in main
    args.func(args)
  File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/scorpio/subcommands/classify.py", line 7, in run
    classify_constellations(options.input,
  File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 567, in classify_constellations
    constellation, variants, rules = parse_variants_in(reference_seq, features_dict, constellation_file,
  File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 349, in parse_variants_in
    variant_list, name, rule_dict = parse_json_in(refseq, features_dict, variants_file, constellation_names, include_ancestral=include_ancestral)
  File "/opt/conda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 225, in parse_json_in
    json_dict = json.load(in_json, strict=False)
  File "/opt/conda/envs/pangolin/lib/python3.8/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/opt/conda/envs/pangolin/lib/python3.8/json/__init__.py", line 370, in loads
    return cls(**kw).decode(s)
  File "/opt/conda/envs/pangolin/lib/python3.8/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/opt/conda/envs/pangolin/lib/python3.8/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 19 column 5 (char 542)

Add NSP2 varint inside variants configuration file

Hello guys, thanks to make all this data available.
I'd like to add aa:NSP2:T85I that I saw inside cB.1.351.json to my variants configuration file for type_variant.py script, but there isn't an option (orf1ab, orf1a, orf1b, s, orf3a, e, m, orf6, orf7a, orf8, n, orf10) for that NSP2 in the type_variants.py.
Could you help me with that?

"s" (lower case) in original json "sites" field

Trying to parse the "sites" field of the json files here:

https://github.com/cov-lineages/constellations/tree/main/constellations/definitions

I found several cases where there should be a "S" (upper case) instead of "s" (lower case) for consistency across mutations (see table below).

Just reporting in case it is useful for you.

sites	Pango_lineages	sites_converted_for_type_variants
s:A570D	B.1.1.7	aa:S:A570D
s:D1118H	B.1.1.7	aa:S:D1118H
s:D1139H	AV.1	aa:S:D1139H
s:D614G	AV.1	aa:S:D614G
s:D80G	AV.1	aa:S:D80G
s:E484K	AV.1	aa:S:E484K
s:G142D	AV.1	aa:S:G142D
s:HV69-	B.1.1.7	aa:S:HV69-
s:I1130V	AV.1	aa:S:I1130V
s:N439K	AV.1	aa:S:N439K
s:N501Y	B.1.1.7	aa:S:N501Y
s:P681H	AV.1	aa:S:P681H
s:P681H	B.1.1.7	aa:S:P681H
s:S982A	B.1.1.7	aa:S:S982A
s:T716I	B.1.1.7	aa:S:T716I
s:T95I	AV.1	aa:S:T95I
s:Y144-	AV.1	aa:S:Y144-
s:Y144-	B.1.1.7	aa:S:Y144-

Split epsilon into 2 constellation files

As per cov-lineages/pangolin#341

WHO label of B.1.526

The definition of B.1.526 contains WHO label ETA. According to https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ (2021-06-08) the WHO-label should be IOTA.

Consistency in json schema

I was hoping to use some of these constellations for a wastewater workflow I am working on and I came across slight inconsistency in the top level descriptor for a couple files. Its pretty minor but the definitions for cAV1.json and cB.1.1.7.json both use "name" while the others use "label". I can easily work around it but I was just curious if this was on purpose?

Create definition for P.4

Would avoid miss classification as related P.1

in-string comment in cBA.1.json keeps breaking backwards-compatibility with scorpio

Hi, in 564121a you reverted comments on definition lines for now, however there is still this strangely formatted line in the new BA.1 definition:

constellations/constellations/definitions/cBA.1.json

Line 25 in feb3b11

"# nuc:G11287T",

This keeps breaking parsing of the file with scorpio 0.3.14 and I wonder what it means. Is that # there on purpose?

Documentation for new components of constellation definitions (incompatible, intermediate)

Hello. We're trying to figure out the recent changes to AY.4.2 calls between versions, and it seems to come down to the 'incompatible lineage' component of the constellation definitions. (v0.0.17...v0.0.20)

Could you please provide a description of what this part of the constellation file means? Also, what are the "intermediate" mutations that are listed? Below are the relevant sections from AY.4:

    "variant": {
	"Pango_lineages": [
	    "AY.4"
	],
	"mrca_lineage": "AY.4",
        "lineage_name": "AY.4",
        "parent_lineage": "B.1.617.2",
        "incompatible_lineage_calls": [
            "AY.4.2"
        ],
	"representative_genome": ""
    },

    ],
    "intermediate": [
        "nuc:G210T:0.976009",
        "nuc:T17040C:0.976009",
        "spike:T95I:0.976009",
        "spike:G142D:0.976009"
    ],

Thanks.

Latest constellations and/or designations creates pangolin failure

Unfortunately i cannot provide the source FASTA file, but using a non-qc-failing FASTA generated by ARTIC with Pangolin supplied by the staphb/pangolin:3.1.16-pangolearn-2021-11-25 image, and then database-updated to:

	2021-12-08T10:17:46.991-08:00 Updating pangolin database...
	2021-12-08T10:18:17.687-08:00 pangolearn already latest release (2021-11-25)
	2021-12-08T10:18:17.687-08:00 constellations updated to v0.0.28
	2021-12-08T10:18:17.687-08:00 pango-designation updated to v1.2.108

Produces the following errors when running Pangolin:

	2021-12-08T10:18:18.820-08:00	Traceback (most recent call last):
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/bin/scorpio", line 8, in <module>
	2021-12-08T10:18:18.820-08:00	sys.exit(main())
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/__main__.py", line 273, in main
	2021-12-08T10:18:18.820-08:00	args.func(args)
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/subcommands/list.py", line 7, in run
	2021-12-08T10:18:18.820-08:00	list_constellations(options.constellations,
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 1080, in list_constellations
	2021-12-08T10:18:18.820-08:00	parse_variants_in(reference_seq, features_dict, constellation_file, constellation_names, label=label)
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 403, in parse_variants_in
	2021-12-08T10:18:18.820-08:00	variant_list, name, output_name, rule_dict, mrca_lineage, incompatible_lineage_calls, parent_lineage, lineage_name = parse_json_in(refseq, features_dict, variants_file, constellation_names, include_ancestral=include_ancestral,label=label,ignore_fails=ignore_fails)
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 283, in parse_json_in
	2021-12-08T10:18:18.820-08:00	record = variant_to_variant_record(site, refseq, features_dict, ignore_fails=ignore_fails)
	2021-12-08T10:18:18.820-08:00	File "/miniconda/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 175, in variant_to_variant_record
	2021-12-08T10:18:18.820-08:00	length = int(lsplit[2])
	2021-12-08T10:18:18.820-08:00	ValueError: invalid literal for int() with base 10: '9 # spike'
	2021-12-08T10:18:18.842-08:00	[Wed Dec 8 18:18:18 2021]
	2021-12-08T10:18:18.842-08:00	Error in rule get_constellations:
	2021-12-08T10:18:18.842-08:00	jobid: 7
	2021-12-08T10:18:18.842-08:00	output: /tmp/tmpainen2l4/get_constellations.txt
	2021-12-08T10:18:18.842-08:00	shell:
	2021-12-08T10:18:18.842-08:00	
	2021-12-08T10:18:18.842-08:00
        scorpio list         --constellations /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cP.3.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cC.37.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cBA.2.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.617.2.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.617.3.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cBA.1_probable.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.525.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cA.23.1.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.617.2+K417N.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cA.23.1+E484K.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.429.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.1.7+E484K.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.617.1.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cP.1.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cAY.4.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.526.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.1.318.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.1.7.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.427.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.351.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cP.2.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.621.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cAV1.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cBA.1.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cB.1.1.529.json /miniconda/envs/pangolin/lib/python3.8/site-packages/constellations/definitions/cAY.4.2.json         --pangolin > /tmp/tmpainen2l4/get_constellations.txt
	2021-12-08T10:18:18.842-08:00	
	2021-12-08T10:18:18.842-08:00	(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
	2021-12-08T10:18:18.843-08:00	Exiting because a job execution failed. Look above for error message

If i do not do the database update, Pangolin runs without error.

I can say that the working run judged the lineage to be AY.39 if that is at all useful.

cB.1.623 excludes all but two B.1.623 representative sequences

PHE was tracking B.1.623+E484K -- which, as far as I can tell, has been observed only once aside from the two British travelers (England/MILK-F9DBDB/2021|EPI_ISL_852237 and England/MILK-F9DB71/2021|EPI_ISL_852169) in the PHE report (where is it referred to as B.1.324.1). B.1.623 is a lot broader (UCSC proposed just B.1 + {S:S494P, S:N501Y, S:P681H, N:M234I}).

As @aretchless pointed out in cov-lineages/pangolin#305 the recent update to pangolin to override pangoLEARN/usher assignments with Scorpio caused most B.1.623 sequences to be assigned 'None' now.

I ran scorpio via pangolin on FASTA for the 739 representative sequences for B.1.623 in pango-designation/lineages.csv:

pangolin --no-temp --outdir B.1.623.reps B.1.623.reps.fa

Only 2 of the 739 reps were classified as cB.1.623:

grep True B.1.623.reps/VOC_report.scorpio.B.1.623-like_counts.csv
England/MILK-F9DB71/2021,0,9,0,0,2,1.000000,0.000000,True
England/MILK-F9DBDB/2021,0,9,0,0,2,1.000000,0.000000,True

The other 737 sequences have too many reference alleles, implying that cB.1.623 is too specific to the virus sequences from those two travelers:

grep False B.1.623.reps/VOC_report.scorpio.B.1.623-like_counts.csv | head
USA/NY-NYULH80/2021,5,3,1,0,0,0.333300,0.555600,False
Aruba/AW-RIVM-11402/2021,6,3,0,0,0,0.333300,0.666700,False
USA/GA-CDC-STM-000009083/2021,6,2,1,0,0,0.222200,0.666700,False
USA/WI-UW-3221/2021,6,2,1,0,0,0.222200,0.666700,False
USA/WI-UW-3271/2021,6,2,1,0,0,0.222200,0.666700,False
USA/NY-PRL-2021_02_15_02F04/2021,5,3,1,0,0,0.333300,0.555600,False
USA/NY-PRL-2021_02_10_02F11/2021,5,3,1,0,0,0.333300,0.555600,False
USA/NY-PRL-2021_02_08_05C09/2021,5,3,1,0,0,0.333300,0.555600,False
USA/NY-PRL-2021_02_08_05F04/2021,5,3,0,1,0,0.333300,0.555600,False
USA/NY-NYULH290/2021,5,3,1,0,0,0.333300,0.555600,False

I suspect the alt_count should be higher than 2 or 3 for those as well (i.e. mutations could be added as well). I will make a pull request that brings cB.1.623.json more in line with my understanding of pango-designation's B.1.623.

Incorrect Definition for C.37

I found an apparent error in the Pango definition for Lambda (C.37). The definition includes the mutation "nuc:T1246I", which is obviously not a nucleotide mutation. It appears to correspond to ORF1ab:T1246I (aka nsp3:T428I) and is encoded by nuc:c4002t.

Add definition constellation for variant Lambda (C.37-like)

Request: co-ordinate release and version tags

Hi,

I don't suppose the release and version tags can be matched to one another?

This would help adding the constellations used to the auto-check and update of dependencies in pangolin: https://github.com/cov-lineages/pangolin/blob/master/pangolin/command.py#L327

Source data

Any chance you could add a link to the raw source data for the genome sequences?

Modifications to B.1.1.529 (Omicron) definition

Remove nuc:C241T - this is in the masked out region of 5' UTR and is always ambiguous in Pangolin alignments
Add spike:Y505H - was being called for reference in some early genomes but seems fixed in Omicron

Remove deletions, del:6513:3 and del:11283:9 ? Deletions are always called badly and the exact positions can be difficult to fix.

BA.1-like vs BA.2

Hi team,
We have 2 sequences from the same sample (SNP distance = 0) : hCoV-19/Australia/QLD2584/2021 and hCoV-19/Australia/QLD2568/2021 but got assigned to different sub-lineage of Omicron using the newest constellations.

taxon	lineage	conflict	ambiguity_score	scorpio_call	scorpio_support	scorpio_conflict	version	pangolin_version	pangoLEARN_version	pango_version	status	note
hCoV-19/Australia/QLD2584/2021	BA.1	0.0	0.9397562119081107	Probable Omicron (BA.1-like)	0.517200	0.258600	PLEARN-v1.2.101	3.1.17	2021-11-25	v1.2.101	passed_qc	scorpio call: Alt alleles 30; Ref alleles 15; Amb alleles 10; Oth alleles 3; scorpio replaced lineage assignment AZ.2
hCoV-19/Australia/QLD2568/2021	BA.2	0.0	1.0	BA.2-like	0.984800	0.015200	PLEARN-v1.2.101	3.1.17	2021-11-25	v1.2.101	passed_qc	scorpio call: Alt alleles 65; Ref alleles 1; Amb alleles 0; Oth alleles 0; scorpio replaced lineage assignment AZ.2

The only difference between 2 sequences is that QLD2568 has better quality than QLD2584. If I run scorpio haplotype against BA.2 constellation, QLD2568 is a perfect match while QLD2584 has only 1 ambiguous allele there.

query	ref_count	alt_count	ambig_count	other_count	support	conflict	orf1ab:S135R	orf1ab:T842I	orf1ab:G1307S	nuc:C4321T	orf1ab:L3027F	nuc:A9424G	orf1ab:T3090I	orf1ab:L3201F	nuc:C10198T	nuc:G10447A	nuc:C12880T	nuc:C15714T	nuc:C15714T	orf1ab:R5716C	orf1ab:T6564I	nuc:A20055G	spike:T19I	del:21633:9	nuc:T22200G	spike:S371F	spike:T376A	spike:D405N	spike:R408S	nuc:C26060T	nuc:C26858T	orf6:D61L	n:S413R
hCoV-19/Australia/QLD2584/2021	0	26	1	0	0.963000	0.000000	R	I	S	T	F	G	I	F	N	A	T	T	T	C	I	G	I	3	G	F	A	N	S	T	T	L	R
hCoV-19/Australia/QLD2568/2021	0	27	0	0	1.000000	0.000000	R	I	S	T	F	G	I	F	T	A	T	T	T	C	I	G	I	3	G	F	A	N	S	T	T	L	R

Please find attached FASTA file for your convenience (QLD2584 has been removed from GISAID due to duplicaiton)
QLD2568-QLD2584.zip

We call it BA.2 but just want let you know the issue.
Thanks,