refine

Refine tandem repeat annotations using a user-defined action file.

This subcommand loads a previously generated annotation and applies a set of manual or scripted corrections (e.g., merging motifs, splitting loci, or adjusting boundaries) specified in an action file.

Usage

vampire refine [options] <prefix> <action_file>

Example

vampire refine results/scan actions.json -o results/scan.revised

Arguments

Argument	Description
prefix	Output prefix of the raw annotation results to refine
action	Action file describing the corrections to apply

Options

Option	Default	Description
-o, --out	<prefix>.revised	Output prefix for refined results
-t, --thread, --threads	8	Number of threads

Output Files

Results are written with the provided output prefix:

• Refined annotation tables and reports after applying the specified actions.