identity

identity#

Calculate sequence identity within tandem repeat regions.

This subcommand computes local sequence identity across TR loci using a sliding motif-level window. It is useful for assessing the purity or divergence of repeat arrays.

Usage#

vampire identity [options] <input_prefix> <output_prefix>

Example#

# Compute identity with default settings
vampire identity results/scan results/identity

# Use a larger window and allow small indels
vampire identity -w 200 --max-indel 2 results/scan results/identity

Arguments#

Argument

Description

prefix

Prefix of the input annotation files

output

Output prefix for identity results

Options#

Option

Default

Description

-w, --window-size

100

Sliding window size (in motifs)

-t, --thread, --threads

30

Number of threads

--mode

raw

Analysis mode: raw or invert

--max-indel

0

Maximum allowed indel length

--min-indel

0

Minimum indel length to consider

Output Files#

Results are written with the provided <output> prefix:

  • Identity tables and visualizations showing local divergence across repeat arrays.

Contents