lsvtool

A small tool to perform comparisons between large structural variants (SVs) from different callers and/or datasets. The input is VCF (*.vcf/*.vcf.gz) files which will be normalized, filtered before being intersected to generate figures.

Tools used:

• SURVIVOR
• truvari
• bcftools
• bedtools

Steps:

• Select non-filtered SV calls (labeled PASS) of correct type (e.g. DEL, INS, INV ...)
• Collapse proximal SV calls using truvari collapse to avoid superfluous calls
• Filter SVs against supplied blacklist, segmental duplications and for size.
• Compare and merge SVs between samples to find intersections.
• Generate heatmaps and venn diagram over sample intersects.
• (OPTIONAL) Benchmark calls against benchmark set of SVs.
• (OPTIONAL) Generate batch files for igv covering regions with the different unique and shared SVs for the samples. Used to plot support in covered regions.

Installation and Running

The installation requires conda environment which will collect all the needed software. So, first make sure you have a working conda!

Installation

git clone https://github.com/HSiga/lsvtool.git  
cd lsvtool  
conda env create -n lsv --file env.yaml 
conda activate lsv  
pip install .  
lsvtool -h

Running analysis

Initialize a working directory

lsvtool init -i file1.vcf.gz file2.vcf.gz.. -o output_directory  
cd output_directory 

Adjust the parameters in the config (parameters.config) file. Finally to run the analysis use_

lsvtool run