![]() ![]() The -mincov option is also available, as in plot. The header and body color can be changed with the -headerColor and -bod圜olor option respectively. However, averaging can be performed that takes the viral loads into account using the -scale_by_viral_load flag. For samples taken the same day, we average the freyja outputs by default. See example title and intro-text files as well. ![]() Where the metadata file should have this form. To update both of these we recommend running the commandįreyja dash -output 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).īy default, this method ships with an existing "data/usher_barcodes.csv" file for the barcodes, and the curated lineage metadata file for summarizing lineages by WHO designation. 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). The value of resid corresponds to the residual of the weighted least absolute devation problem used to estimate lineage abundances. The lineage array lists the identified lineages in descending order, and abundances contains the corresponding abundances estimates. ![]() B.1.617.2 and AY.6 abundances are summed in the above example), otherwise they are grouped into "Other". Where summarized denotes a sum of all lineage abundances in a particular WHO designation (i.e. For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided using the -meta option. As the UShER tree now included proposed lineages, we now offer the -confirmedonly flag which removes unconfirmed lineages from the analysis. A custom barcode file can be provided using the -barcodes option. This method also includes a -eps option, which enables the user to define the minimum lineage abundance returned to the user (e.g. This outputs to a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation. ![]()
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