bio-workflows-longread-sv-pipeline

You can detect structural variants from long-read sequencing data by running an end-to-end pipeline that applies QC, alignment with minimap2, SV calling using Sniffles or cuteSV, and optional annotation to produce a VCF file and QC reports.

Yes, the structural variant pipeline works with both ONT and PacBio data, automatically applying the appropriate mapper and caller settings for nanopore and HiFi reads to ensure accurate SV detection.

The best way to merge structural variant calls across multiple samples is to use a pipeline that supports joint analysis, allowing you to combine SV calls from Sniffles or cuteSV outputs for multi-sample evaluation.

Yes, you need minimap2 and Sniffles and/or cuteSV installed to run the long-read SV pipeline, as these tools handle the read alignment and structural variant calling processes required to generate the final VCF output.

Yes, you can annotate structural variants detected by cuteSV or Sniffles using optional annotation tools integrated into the pipeline, adding context to the filtered VCF of SV calls for downstream analysis.