| Name | sniffles2-plot JSON |
| Version |
0.2.1
JSON |
| download |
| home_page | None |
| Summary | a visualizer tool for plot generating |
| upload_time | 2024-08-18 20:50:18 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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| Travis-CI |
No Travis.
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# 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:
<img src="./pictures/del_ins_type_size.jpg" width="200" height="200">
<img src="./pictures/hetamap.jpg" width="200" height="200">
<img src="./pictures/length_variant.jpg" width="200" height="200">
<img src="./pictures/sample_upset.png" width="200" height="200">
Raw data
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"description": "# Sniffles Plot\n\n## Introduction\n\nThe Sniffle Plot is a Python program that generates plots for single and multi-sample VCF files.\n\nType of plots for single sample VCF file:\n\n1. Variant Frequency Spectrum\n2. Genotype Frequency\n3. SV Size & Type Distribution\n4. Comparison of Length of Variants\n\nType of plots for multi samples VCF file:\n \n1. Variant Frequency Spectrum\n2. Upset plot for sample intersection\n3. SV sites per genome\n4. Variant call all SVs\n5. Size distribution\n6. Heat map for deletion and insertion intersections\n\n\n\n## Quick Start\nTo install this package you can simply run the following command:\n```\n$ pip3 install sniffles2-plot\n```\n\nFor running the program for multiple vcf files located in a sepcific directory:\n```\n$ python3 -m sniffles2_plot -i <VCF_files_folder>\n``` \n \nFor running the program for a single vcf file:\n```\n$ python3 -m sniffles2_plot -i <file_name> -o <output_folder>\n```\nSample results of output:\n\n<img src=\"./pictures/del_ins_type_size.jpg\" width=\"200\" height=\"200\">\n<img src=\"./pictures/hetamap.jpg\" width=\"200\" height=\"200\">\n\n<img src=\"./pictures/length_variant.jpg\" width=\"200\" height=\"200\">\n<img src=\"./pictures/sample_upset.png\" width=\"200\" height=\"200\">\n\n\n",
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