The pipeline calls structural variants from aligned long sequencing reads (PacBio HiFi, ONT, ONT ultralong) using three SV callers: cuteSV, sniffles and SVIM. It additionally filters the calls, creates a merged callset and generates some plots comparing the sets. Variant calls for HG002 are additionally evaluated based on the GIAB medically relevant SVs.
For each BAM file to be analyzed, the path to the corresponding BAM file must be specified in config/config.yaml, together with a sample name, the coverage and the sequencing technology ("hifi", "ont" or "ont-ul").
Furthermore, the path to the reference sequence used must be added to the config file.
The pipeline can then be run using the following command:
snakemake -j <nr_cores>