odgi pav

Presence/absence variants (PAVs). It prints to stdout a TSV table with the PAV ratios. For a given path range PR and path P, the PAV ratio is the ratio between the sum of the lengths of the nodes in PR that are crossed by P divided by the sum of the lengths of all the nodes in PR.

SYNOPSIS

odgi pav [-i, --idx=FILE] [-b, –bed-file=FILE] [OPTION]…

DESCRIPTION

The odgi pav command prints to stdout a matrix with the Presence/absence variants (PAVs) ratios.

OPTIONS

MANDATORY OPTIONS

-i, --idx=FILE

Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!

-b, --bed-file=FILE

Find PAVs in the path range(s) specified in the given BED FILE

Pav Options

-p, --path-groups=FILE

Group paths as described in two-column FILE, with columns path.name and group.name.

-S, --group-by-sample

Following PanSN naming (sample#hap#ctg), group by sample (1st field).

-H, --group-by-haplotype

Following PanSN naming (sample#hap#ctg), group by haplotype (2nd field).

-B, --binary-values=THRESHOLD

Print 1 if the PAV ratio is greater than or equal to the specified THRESHOLD, else 0.

-M, --matrix-output

Emit the PAV ratios in a matrix, with path ranges as rows and paths/groups as columns.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the components and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi pav.