C-G.15: Extending the megSAP pipeline for medical genetics to long-read sequencing
Author
Keywords
medical genetics, rare disease, sequence analysis pipeline
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megSAP is an open-source sequence data analysis pipeline for rare disease and oncology. Since its initial development in 2016, the pipeline has been continuously refined to incorporate advances in short-read analysis for Illumina sequencing data.
Since 2024, functionality has been progressively added to support long-read technologies from Oxford Nanopore Technologies and PacBio.
This includes technology-specific mapping and variant-calling tools, as well as support for methylation analysis and haplotype phasing based on long-read data.
Consistent with its short-read workflow, megSAP enables comprehensive detection of major variant classes, including single-nucleotide variants and small indels, copy number variants, structural variants, and repeat expansions.
The resulting variant lists are extensively annotated and optimized for downstream interpretation in a clinical genetics setting.
megSAP also supports multi-sample analyses, for example in trio settings. This functionality has been extended to allow the combined analysis of short-read and long-read variants for small variants and copy-number variants.
Support for mixed analyses of structural variants is not yet available.
megSAP is freely available at https://github.com/imgag/megSAP
Co-authors: Tobias Haack, Stephan Ossowski, Leon Schütz
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