freyja covariants

Finds mutations co-occurring on the same read pair in BAM_FILE between MIN_SITE and MAX_SITE

freyja covariants [OPTIONS] INPUT_BAM [MIN_SITE] [MAX_SITE]

Options

--output <output>

path to save co-occurring mutations

Default:

covariants.tsv

--ref-genome <ref_genome>

Default:

data/NC_045512_Hu-1.fasta

--annot <annot>

path to gff file corresponding to reference genome. If included, outputs amino acid mutations in addition to nucleotide mutations.

--min_quality <min_quality>

minimum quality for a base to be considered

Default:

20

--min_count <min_count>

minimum count for a set of mutations to be saved

Default:

10

--spans_region

if included, consider only reads that span the region defined by (min_site, max_site)

Default:

False

--sort_by <sort_by>

method by which to sort covariants patterns. Set to “count” or “freq” to sort patterns by count or frequency (in descending order). Set to “site” to sort patterns by start site (n ascending order).

Default:

count

--threads <threads>

number of parallet processes to use. Recommended for large BAM files.

Default:

1

Arguments

INPUT_BAM

Required argument

MIN_SITE

Optional argument

MAX_SITE

Optional 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). Should the user wish to only consider read pairs that span the entire genomic region defined by (min_site, max_site), they may include the --spans_region flag. By default, the covariant patterns are sorted in descending order by count, however they can also be sorted in descending order by frequency by setting the --sort_by option to “freq”, or sorted sequentially by mutation site by setting the --sort_by option to “site”. The --ref-genome 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 --ref-genome instead. Optionally, a gff file (e.g. freyja/data/NC_045512_Hu-1.gff) may 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.