Closed ArtPoon closed 2 months ago
[covizu@Paphlagon data]$ unxz -c provision.2024-04-13T00\:00\:06.json.xz | grep -c "\"covv_lineage\": \"BA.2.86\""
947
=# select count(accession) from sequences where lineage='BA.2.86';
count
-------
916
(1 row)
It looks like we have 916 records in the database. Checking to see if these sequences are being filtered
Of the 918 BA.2.86 records that made it to the filter_problematic
function:
850 sequences were filtered out as being outliers, 65 were filtered out for having a lot of missing sites
Ok I think we have to turn off molecular clock filtering for now. Let's do the following:
cutoff=0
to filter_problematic
qp = None
if cutoff==0
around line:
qp = QPois(quantile=1-cutoff, rate=rate, maxtime=maxtime, origin=origin)
if qp.is_outlier(coldate, ndiffs):
to if qp and qp.is_outlier(coldate, ndiffs):
to skip test if qp
is NoneAlternatively it might be easier to modify QPois
to return False
for every call to is_outlier
when it is initialized with cutoff=0
Reprocessing everything in the database to update variants with this change
Currently we are only displaying 3 samples categorized as BA.2.86:![image](https://github.com/PoonLab/covizu/assets/1109328/d481b966-c5d9-4ec4-9f49-aab821d23aae)
However the GISAID database currently holds 776 records with this lineage label.