identity

Table of contents

1. Introduction
2. Input and Output
   1. Input
   2. Output
3. Usage Examples
   1. 1. plot raw identity heatmap
   2. 2. plot inverted identity heatmap
   3. 3. plot identity heatmap including INDELs
4. Parameters

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Introduction

The identity command in VAMPIRE is designed to calculate the self-identity of one TR sequence.

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Input and Output

Input

Input	Format	Description	Default
Annotation	TSV	Detailed annotation results from anno command	None
Motif	TSV	Statistics of detected motifs from anno command	None

Output

Output	Format	Description	Default
Identity Matrix	BED	Identity between two windows	None

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Usage Examples

1. plot raw identity heatmap

vampire identity -t 30 -w 30 annotation_prefix output_prefix

2. plot inverted identity heatmap

vampire identity -t 30 -w 30 --mode="invert" annotation_prefix output_prefix

3. plot identity heatmap including INDELs

vampire identity -t 30 -w 30 --min-indel 1 --max-indel 10 annotation_prefix output_prefix

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Parameters