freyja covariants

Calls physically linked mutations in BAM_FILE using coVar (https://github.com/andersen-lab/covar)

freyja covariants [OPTIONS] INPUT_BAM

Options

--reference <reference>

Default:

data/NC_045512_Hu-1.fasta

--annot <annot>

path to gff file corresponding to reference genome

Default:

data/NC_045512_Hu-1.gff

--start_site <start_site>

minimum genomic coordinate to consider

Default:

0

--end_site <end_site>

maximum genomic coordinateto consider (defaults to full genome)

--output <output>

Default:

covariants.tsv

--min_quality <min_quality>

minimum quality for a base to be considered

Default:

20

--min_depth <min_depth>

minimum count for a set of mutations to be saved

Default:

10

--threads <threads>

number of threads to use

Default:

1

Arguments

INPUT_BAM

Required argument

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Example Usage:

In many cases, it can be useful to study covariant mutations (i.e. mutations co-occurring on the same read pair). This outputs to a tsv file that includes the mutations present in each set of covariants, their absolute counts (the number of read pairs with the mutations), their coverage ranges (the minimum and maximum position for read-pairs with the mutations), their “maximum” counts (the number of read pairs that span the positions in the mutations), and their frequencies (the absolute count divided by the maximum count). The --reference argument defaults to freyja/data/NC_045512_Hu-1.fasta. If you are using a different build to perfrom alignment, it is important to pass that file in to --reference instead. Additionally, a gff file (e.g. freyja/data/NC_045512_Hu-1.gff) must be included via the --annot option to output amino acid mutations alongside nucleotide mutations. Inclusion thresholds for read-mapping quality and the number of observed instances of a set of covariants can be set using --min_quality and --min_count respectively.