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VISTA: An integrated framework for structural variant discovery

VISTA is an integrated SV calling framework that leverages results of individual callers using a novel and robust filtering and merging algorithm.

Installation

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

Prerequisites

  • python 3.8
pip install PyVCF
pip install matplotlib

Usage

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

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

Command-line Options

  • -h, --help: Show the help message and exit.

  • -i INPUTS, --inputs: Input VCF files to be merged

  • -s SAMPLE, --sample: Specify the sample type, either "mouse" or "human"

  • -o OUTPUT, --output: Ouptut folder where VISTA will be saved

  • -g GOLD, --gold: Provide the path to gold standard VCF file

  • -a, --analysis: If this flag is included, it reports statistics

  • -t, --threshold: threshold number for comparison

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