CallSV

This repo provides a simple pipeline for calling Structural Variants (SVs) from long-read alignments.

Dependencies

• Sniffles
• Iris
• Minimap2
• Samtools
• Racon
• Jasmine

Installation

If executables for the above dependencies are not in one's PATH, they can be manually added to the bash scripts.

Run

For each sample, call SVs by running ./call_hifi.sh for PacBio HiFi read alignments or ./call_ont.sh for Oxford Nanopore read alignments.

To merge SV calls across samples, use ./merge.sh