generator

Table of contents

  1. Introduction
  2. Input and Output
    1. Input
    2. Output
  3. Usage Examples
    1. 1. Generate a simple TR sequence
    2. 2. Generate a TR sequence with multiple motifs
  4. Parameters

Introduction

The generator command in VAMPIRE is designed to generate simulated tandem repeat sequence with user-defined motifs, length and mutation rate. Random seed can be set to enable reproductive results.

Input and Output

Input

Input Format Description Default
Motifs string (parameter) One motif or a list of motifs to generate the sequence None
Length integer (parameter) Length of the simulated sequence None
Mutation Rate float (parameter) Mutation rate for SNVs and INDELs None
Seed integer (parameter) Random seed for reproducibility 42

Output

Output Format Description Default
Sequence FASTA Simulated tandem repeat sequence None
Annotation TSV Annotation file with mutations None
Annotation_woMut TSV Annotation file before introducing mutations None

Usage Examples

1. Generate a simple TR sequence 

vampire generator -m GGC -l 1000 -r 0.01 -p simulated_TR

2. Generate a TR sequence with multiple motifs 

vampire generator -m AATGG CCATT -l 1000 -r 0.01 -p simulated_TR

Parameters