freyja demix

Generate relative lineage abundances from VARIANTS and DEPTHS

freyja demix [OPTIONS] VARIANTS DEPTHS

Options

--eps <eps>

minimum abundance to include for each lineage

Default:

0.001

--barcodes <barcodes>

Path to custom barcode file

--meta <meta>

custom lineage to variant metadata file

--output <output>

Output file

Default:

demixing_result.tsv

--covcut <covcut>

calculate percent of sites with n or greater reads

Default:

10

--confirmedonly

exclude unconfirmed lineages

Default:

False

--version

Default:

False

--depthcutoff <depthcutoff>

exclude sites with coverage depth below this value andgroup identical barcodes

Default:

0

--lineageyml <lineageyml>

lineage hierarchy file in a yaml format

--adapt <adapt>

adaptive lasso penalty parameter

Default:

0.0

--a_eps <a_eps>

adaptive lasso parameter, hard threshold

Default:

1e-08

--region_of_interest <region_of_interest>

JSON file containing region(s) of interest for which to compute additional coverage estimates

--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

--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 | H1N1pdm | FLU-B-VIC | MEASLESN450 | MEASLES | RSVa | RSVb

--autoadapt

use error profile to set adapt

Default:

False

Arguments

VARIANTS

Required argument

DEPTHS

Required argument

---

Example Usage:

After running freyja variants we can run: freyja demix [variants-file] [depth-file] --output [output-file]

This outputs to a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation. This method also includes a --eps option, which enables the user to define the minimum lineage abundance returned to the user (e.g. --eps 0.0001). A custom barcode file can be provided using the --barcodes [path-to-barcode-file] option. By default, freyja uses the lineage hierarchy file located infreyja/data directory which is updated everytime the freyja update command is run. The user, however, can define a custom lineage hierarchy file using--lineageyml [path-to-lineage-file]. Users can get the historic lineage.yml file at freyja-data GitHub repository here. As the UShER tree now included proposed lineages, we now offer the --confirmedonly flag which removes unconfirmed lineages from the analysis. For additional flexibility and reproducibility of analyses, a custom lineage-to-constellation mapping metadata file can be provided using the --meta option. A coverage depth minimum can be specified using the --depthcutoff option, which excludes sites with coverage less than the specified value. An example output should have the format

	filename
summarized	[(‘Delta’, 0.65), (‘Other’, 0.25), (‘Alpha’, 0.1)]
lineages	[‘B.1.617.2’ ‘B.1.2’ ‘AY.6’ ‘Q.3’]
abundances	“[0.5 0.25 0.15 0.1]”
resid	3.14159
coverage	95.8

Where summarized denotes a sum of all lineage abundances in a particular WHO designation (i.e. B.1.617.2 and AY.6 abundances are summed in the above example), otherwise they are grouped into “Other”. The lineage array lists the identified lineages in descending order, and abundances contains the corresponding abundances estimates. Using the --depthcutoff option may result in some distinct lineages now having identical barcodes, which are grouped into the format [lineage]-like(num) (based on their shared phylogeny) in the output. A summary of this lineage grouping is outputted to [output-file]_collapsed_lineages.yml. The value of resid corresponds to the residual of the weighted least absolute deviation problem used to estimate lineage abundances. The coverage value provides the 10x coverage estimate (percent of sites with 10 or greater reads- 10 is the default but can be modfied using the --covcut option in demix). If there is an solver error during the demix step (generally associated with poor data quality), an error message will be returned, along with an output empty summarized, lineages, and abundances, and with resid = -1.

NOTE: The freyja variants output is stable in time, and does not need to be re-run to incorporate updated lineage designations/corresponding mutational barcodes, whereas the outputs of freyja demix will change as barcodes are updated (and thus demix should be re-run as new information is made available).