freyja relgrowthrate
Calculates relative growth rates for each lineage using AGG_RESULTS and METADATA
freyja relgrowthrate [OPTIONS] AGG_RESULTS METADATA
Options
- --thresh <thresh>
min lineage abundance in plot
- Default:
0.01
- --scale_by_viral_load
scale by viral load
- Default:
False
- --nboots <nboots>
Number of Bootstrap iterations
- Default:
1000
- --serial_interval <serial_interval>
Serial Interval
- Default:
5.5
- --config <config>
control the colors and grouping of lineages in the plot
- --mincov <mincov>
min genome coverage included
- Default:
60.0
- --output <output>
Output html file
- Default:
rel_growth_rates.csv
- --days <days>
number of days for growth calculation
- Default:
56
- --grthresh <grthresh>
minimum prevalence to calculate relative growth rate for
- Default:
0.001
- --lineageyml <lineageyml>
lineage hierarchy file
- --pathogen <pathogen>
Pathogen of interest.Not used if using –lineageyml option.
- Default:
SARS-CoV-2- Options:
SARS-CoV-2 | MPXV | H5NX | H1N1pdm | FLU-B-VIC | MEASLESN450 | MEASLES | RSVa | RSVb
Arguments
- AGG_RESULTS
Required argument
- METADATA
Required argument
Example Usage:
This command will generate the relative growth rates for each
Lineage and output it as a CSV file. The lineages can also be grouped
together by passing the --config [path-to-plot-config-file] option.
This uses the same configuration file as the dash command. The
lineages are grouped together based on the Lineage: field in the
config file. The number of bootstraps can be specified with the
--nboots [number-of-bootstraps] option and the serial interval can
be specified with the --serial_interval option. The output will be a
CSV file with the following columns:
Lineage |
Estimated Advantage |
Bootstrap 95% interval |