freyja boot

Perform bootstrapping method for freyja using VARIANTS and DEPTHS

freyja boot [OPTIONS] VARIANTS DEPTHS

Options

--nb <nb>

number of times bootstrapping is performed

Default:

100

--nt <nt>

max number of cpus to use

Default:

1

--eps <eps>

minimum abundance to include

Default:

0.001

--barcodes <barcodes>

custom barcode file

--meta <meta>

custom lineage to variant metadata file

--output_base <output_base>

Output file basename

Default:

test

--boxplot <boxplot>

file format of boxplot output (e.g. pdf or png)

--confirmedonly

exclude unconfirmed lineages

Default:

False

--rawboots

return raw bootstraps

Default:

False

--lineageyml <lineageyml>

lineage hierarchy file in yaml format

--depthcutoff <depthcutoff>

exclude sites with coverage depth below this value andgroup identical barcodes

Default:

0

--relaxedmrca

for use with depth cutoff,clusters are assigned robust mrca to handle outliers

Default:

False

--relaxedthresh <relaxedthresh>

associated threshold for robust mrca function

Default:

0.9

--bootseed <bootseed>

set seed for bootstrap generation

Default:

0

--solver <solver>

solver used for estimating lineage prevalence

Default:

CLARABEL

--pathogen <pathogen>

Pathogen of interest.Not used if using –barcodes option.

Default:

SARS-CoV-2

Options:

SARS-CoV-2 | MPXV | H5NX | H5NX-cattle | H1N1pdm | FLU-B-VIC | H3N2 | MEASLESN450 | MEASLES | RSVa | RSVb | DENV1 | DENV2 | DENV3 | DENV4

--autoadapt

use error profile to set adapt

Default:

False

--freqcol <freqcol>

Frequency column name in the vcf file

Default:

AF

Arguments

VARIANTS

Required argument

DEPTHS

Required argument

---

Example Usage:

We provide a fast bootstrapping method for freyja, which can be run using the command

freyja boot [variants-file] [depth-file] --nt [number-of-cpus] --nb [number-of-bootstraps] --output_basename [base-name]

which results in two output files: base-name_lineages.csv and base-name_summarized.csv, which contain the 0.025, 0.05, 0.25, 0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage and WHO designated VOI/VOC, respectively, as obtained via the bootstrap. A custom lineage hierarchy file can be provided using --lineageyml option. If the --rawboots option is used, it will return two additional output files base-name_lineages_boot.csv and base-name_summarized_boot.csv, which contain the bootstrap estimates (rather than summary statistics). We also provide the --eps, --barcodes, and --meta options as in freyja demix. We now also provide a --boxplot option, which should be specified in the form --boxplot pdf if you want the boxplot in pdf format.