anno

Table of contents

  1. Introduction
  2. Input and Output
    1. Input
    2. Output
  3. Usage Examples
    1. 1. de novo annotate
    2. 2. decompose using a consensus motif or a motif set
    3. 3. annotate population-level sequence
  4. Parameters

Introduction

The anno command in VAMPIRE is designed to annotate tandem repeat loci with detailed motif information and variation patterns.

By providing a FASTA file containing tandem repeat loci, anno generates a list of annotated TSV file. These files are the input for evaluate, refine, logo, identity command.

Input and Output

Input

Input Format Description Default
Sequence FASTA The sequence to be annotated None
Motif DB FASTA Motif database used to refine and align motifs during analysis base

Output

Output Format Description Default
Config JSON Parameter set used for the annotation job None
Annotation TSV Detailed annotation results None
Concise TSV Summary of annotation results None
Motif TSV Statistics of detected motifs None
Distance TSV Edit distances between detected motifs None

Usage Examples

1. de novo annotate

Annotate tandem repeat loci directly from a FASTA file, discovering motifs automatically.

vampire anno [parameters] repeats.fasta annotation_prefix

2. decompose using a consensus motif or a motif set

Decompose tandem repeats using a provided consensus motif or motif set, without de novo motif discovery.

vampire anno [parameters] --no-denovo -m consensus_motif.fasta repeats.fasta annotation_prefix

3. annotate population-level sequence

Annotating tandem repeat (TR) loci at the population level can be challenging due to highly variable copy numbers among individuals. For loci with low copy numbers, accurate annotation is more difficult. In such cases, providing a curated motif set can improve annotation quality and consistency across samples. A three-step strategy can be applied:

STEP-1: Call the motif set from the population sequences

vampire anno [parameters] population_sequences.fasta population_annotation

STEP-2: Create a motif database from the annotation

vampire mkref population_annotation population_motif_set.fasta

STEP-3: Use the curated motif database to annotate the population sequences

vampire anno [parameters] --no-denovo -m population_motif_set.fasta population_sequences.fasta population_annotation.curated

Parameters