Decide on reasonable min-length filter

[j23414]

Context

Noticed some WA samples were being dropped due to the min-length filter (originally set to include at least 90% of the genome or 9800nt). We're considering dropping that lower to include more sequences as long as the phylogenetic tree looks reasonable.

The augur index of the WA sequences: wa_stats.txt

[j23414]

Just documenting that min-length can be adjusted in the following locations:

Washington-specific

WNV/phylogenetic/build-configs/washington-state/config.yaml

Lines 15 to 20 in ea9ec0e

	subsampling:
	state: --query "state == 'WA'" --min-length '9800' --subsample-max-sequences 5000
	neighboring_state: --query "state in ['CA', 'ID', 'OR', 'NV']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
	region: --query "state in ['AZ','NM', 'CO', 'UT', 'WY', 'MT']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
	country: --query "country == 'USA' and state not in ['WA', 'CA', 'ID', 'OR', 'NV','AZ','NM', 'CO', 'UT', 'WY', 'MT'] and accession != 'NC_009942'" --group-by state year --subsample-max-sequences 300 --min-length '9800'
	force_include: --exclude-all --include ../nextclade/defaults/include.txt

global

WNV/phylogenetic/defaults/config.yaml

Lines 67 to 69 in ea9ec0e

	subsampling:
	region: --query "is_lab_host != 'true'" --query-columns is_lab_host:str --min-length '9800' --group-by region year --subsample-max-sequences 3000 --exclude defaults/exclude.txt
	force_include: --exclude-all --include defaults/include.txt