[Request An Update]: Pangolin (constellations)

[garfinjm]

Contact Details

No response

What container needs an update?

The constelations version in the Pangolin container is causing some issues in our lab and at least one other lab in our region, the v0.1.9 and v0.1.10 updates fix a bug that causes genomes with lots of missing data to be mis-assigned as probable BA.x by Scorpio (some details here: cov-lineages/pango-designation#584)

Thanks for all your work on this!

[kapsakcj]

I'll push a hotfix as soon as I'm able. thanks for raising the issue!

[kapsakcj]

I've made a dev branch with this change cjk-pango-constellations-bugfix. Have not built a new docker image yet though

But this issue has me a little worried: cov-lineages/pangolin#449

Are you seeing anything similar? Lots of samples being that were previously given lineages to "Unassigned"?

[kapsakcj]

@garfinjm the docker image is available on dockerhub and quay now: staphb/pangolin:4.0.6-pdata-1.8-constellations-0.1.10 . Would love to hear more feedback on how it goes!

[garfinjm]

Here's a test on the 11 samples that I had posted in cov-lineages/pango-designation#584 that were all originally mis-called as BA.3. Everything seems like it's working to me, thanks for putting together the new image!

staphb/pangolin:4.0.6-pdata-1.8

taxon	lineage	conflict	ambiguity_score	scorpio_call	scorpio_support	scorpio_conflict	scorpio_notes	version	pangolin_version	scorpio_version	constellation_version	is_designated	qc_status	qc_notes	note
A	BA.3			Probable Omicron (BA.3-like)	0.54	0.07	scorpio call: Alt alleles 29; Ref alleles 4; Amb alleles 21; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.42	scorpio called lineage BA.3
B	BA.3			Probable Omicron (BA.3-like)	0.46	0.04	scorpio call: Alt alleles 25; Ref alleles 2; Amb alleles 26; Oth alleles 1	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.37	scorpio called lineage BA.3
C	BA.3			Probable Omicron (BA.3-like)	0.56	0.09	scorpio call: Alt alleles 30; Ref alleles 5; Amb alleles 19; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.38	scorpio called lineage BA.3
D	BA.3			Probable Omicron (BA.3-like)	0.46	0.02	scorpio call: Alt alleles 25; Ref alleles 1; Amb alleles 28; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.44	scorpio called lineage BA.3
E	BA.3			Probable Omicron (BA.3-like)	0.46	0.02	scorpio call: Alt alleles 25; Ref alleles 1; Amb alleles 28; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.45	scorpio called lineage BA.3
F	BA.3			Probable Omicron (BA.3-like)	0.39	0.04	scorpio call: Alt alleles 21; Ref alleles 2; Amb alleles 31; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.63	scorpio called lineage BA.3
G	BA.3			Probable Omicron (BA.3-like)	0.54	0.07	scorpio call: Alt alleles 29; Ref alleles 4; Amb alleles 21; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.43	scorpio called lineage BA.3
H	BA.3			Probable Omicron (BA.3-like)	0.54	0.07	scorpio call: Alt alleles 29; Ref alleles 4; Amb alleles 21; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.43	scorpio called lineage BA.3
I	BA.3			Probable Omicron (BA.3-like)	0.54	0.07	scorpio call: Alt alleles 29; Ref alleles 4; Amb alleles 21; Oth alleles 0	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.42	scorpio called lineage BA.3
J	BA.3			Probable Omicron (BA.3-like)	0.54	0.06	scorpio call: Alt alleles 29; Ref alleles 3; Amb alleles 21; Oth alleles 1	SCORPIO_v0.1.8	4.0.6	0.3.17	v0.1.8	FALSE	fail	Ambiguous_content:0.42	scorpio called lineage BA.3

4.0.6-pdata-1.8-constellations-0.1.10

taxon	lineage	conflict	ambiguity_score	scorpio_call	scorpio_support	scorpio_conflict	scorpio_notes	version	pangolin_version	scorpio_version	constellation_version	is_designated	qc_status	qc_notes	note
A	Unassigned			Probable Omicron (Unassigned)	0.61	0	scorpio call: Alt alleles 20; Ref alleles 0; Amb alleles 13; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.42
B	Unassigned			Probable Omicron (Unassigned)	0.48	0	scorpio call: Alt alleles 16; Ref alleles 0; Amb alleles 17; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.37
C	Unassigned			Probable Omicron (Unassigned)	0.64	0	scorpio call: Alt alleles 21; Ref alleles 0; Amb alleles 12; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.38
D	Unassigned			Probable Omicron (Unassigned)	0.48	0	scorpio call: Alt alleles 16; Ref alleles 0; Amb alleles 17; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.44
E	Unassigned			Probable Omicron (Unassigned)	0.48	0	scorpio call: Alt alleles 16; Ref alleles 0; Amb alleles 17; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.45
F	Unassigned			Probable Omicron (Unassigned)	0.36	0	scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 21; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.63
G	Unassigned			Probable Omicron (Unassigned)	0.61	0	scorpio call: Alt alleles 20; Ref alleles 0; Amb alleles 13; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.43
H	Unassigned			Probable Omicron (Unassigned)	0.61	0	scorpio call: Alt alleles 20; Ref alleles 0; Amb alleles 13; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.43
I	Unassigned			Probable Omicron (Unassigned)	0.61	0	scorpio call: Alt alleles 20; Ref alleles 0; Amb alleles 13; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.42
J	Unassigned			Probable Omicron (Unassigned)	0.61	0	scorpio call: Alt alleles 20; Ref alleles 0; Amb alleles 13; Oth alleles 0	PUSHER-v1.8	4.0.6	0.3.17	v0.1.10	FALSE	fail	Ambiguous_content:0.42

[kapsakcj]

OK great, thanks for sharing. So these failed QC, but were still assigned BA.3 via scorpio in the older docker image? (staphb/pangolin:4.0.6-pdata-1.8)

Are you running pangolin with lower-than-default --max-ambig ?

[garfinjm]

Yeah, these are all terrible genomes, but they were all called BA.3 which hasnt shown up yet in MN. I got really suspicious when I had 11 on a single run of 92 samples back in April.

We are using a pretty barebones pangolin command:
pangolin -t 1 --analysis-mode accurate --outfile pusher_!{fasta}.csv !{fasta}