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PyVista package #1

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20 changes: 19 additions & 1 deletion README.md
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Expand Up @@ -4,12 +4,19 @@ VISTA is an integrated SV calling framework that leverages results of individual

## Installation

#### Option A: Install the Python Package

```shell
pip install git+https://github.com/nahid18/VISTA.git
```
#### Option B: Clone and Run

```shell
git clone https://github.com/Addicted-to-coding/VISTA/tree/main
cd VISTA
```

## Prerequisites
##### Prerequisites
- python 3.8

```shell
Expand All @@ -19,12 +26,23 @@ pip install matplotlib

## Usage

If you installed the `python` package, run this command from terminal:
```shell
vista
```

If you cloned the original repository, then follow this:

`python vista.py -i [MANTA VCF] [LUMPY VCF] [DELLY VCF] [GENOMESTRIP VCF] [CLEVER VCF] [POPDEL VCF] [OCTOPUS VCF] -s [mouse or human] -o [output folder]`

- Note: Input files' tool names should be all in lowercase

## EXAMPLE

- `vista -i manta_HG002.vcf delly_HG002.vcf genomestrip_HG002.vcf octopus_HG002.vcf -o ./results -s human`

or,

- `python vista.py -i manta_HG002.vcf delly_HG002.vcf genomestrip_HG002.vcf octopus_HG002.vcf -o ./results -s human`

## Command-line Options
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