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CallSV

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

Dependencies

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