Sniffles Plot

Introduction

The Sniffle Plot is a Python program that generates plots for single and multi-sample VCF files.

Type of plots for single sample VCF file:

1. Variant Frequency Spectrum
2. Genotype Frequency
3. SV Size & Type Distribution
4. Comparison of Length of Variants

Type of plots for multi samples VCF file:

1. Variant Frequency Spectrum
2. Upset plot for sample intersection
3. SV sites per genome
4. Variant call all SVs
5. Size distribution
6. Heat map for deletion and insertion intersections

Quick Start

To install this package you can simply run the following command:

$ pip3 install sniffles2-plot

For running the program for multiple vcf files located in a sepcific directory:

$ python3 -m sniffles2_plot -i <VCF_files_folder>

For running the program for a single vcf file:

$ python3 -m sniffles2_plot -i <file_name> -o <output_folder>

Sample results of output: