freyja get-lineage-def

Get the mutations defining a LINEAGE of interest from provided barcodes

freyja get-lineage-def [OPTIONS] LINEAGE

Options

--barcodes <barcodes>

Path to custom barcode file

Default:: data/usher_barcodes.feather

--annot <annot>: Path to annotation file in gff3 format. If included, shows amino acid mutations.

--ref <ref>: Reference file in fasta format. Required to display amino acid mutations

--output <output>: Output file to save lineage definition. Defaults to stdout.

Arguments

LINEAGE: Required argument

Example Usage:

This command fetches the lineage-defining mutations for the specified lineage. Defaults to stdout if no output file is specified.

freyja get-lineage-def B.1.1.7
C241T
C913T
C3037T
C3267T
C5388A
(cont...)

If a gene annotation file (gff3) is provided along with a reference genome (fasta), the mutations will include the respective amino acid changes for non-synonymous mutations.

freyja get-lineage-def BA.2.12 --annot freyja/data/NC_045512_Hu-1.gff --ref freyja/data/NC_045512_Hu-1.fasta
...
C21618T(S:T19I)
T22200G(S:V213G)
G22578A(S:G339D)
C22674T(S:S371F)
T22679C(S:S373P)
C22686T(S:S375F)
A22688G(S:T376A)
G22775A(S:D405N)
A22786C(S:R408S)
G22813T(S:K417N)
(cont...)