Aug 28, 2025
Long read variant calling protocol using Sniffles
- Katherine Wang1,
- Thomas Karathanos1
- 1Stanford University
- tk-protocols-for-upload
Protocol Citation: Katherine Wang, Thomas Karathanos 2025. Long read variant calling protocol using Sniffles. protocols.io https://dx.doi.org/10.17504/protocols.io.261gek5bdg47/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
The method was used for a bioinformatics analysis
Created: August 28, 2025
Last Modified: August 28, 2025
Protocol Integer ID: 225678
Keywords: sequencing data, variant calling protocol, calling pipeline, abbreviated description
Abstract
Abbreviated description of variant calling pipeline for long read whole genome sequencing data.
Troubleshooting
Prerequisites
Long read whole genome sequencing of adenocarcinoma, polyp, and normal samples was conducted.
Bioinformatics analysis
SVs were called with Sniffles v2.2 using default parameters along with the --snf tag.
Software version URL: https://github.com/fritzsedlazeck/Sniffles/releases/tag/v2.2
To compare SV calls across the adenocarcinoma, polyp, and normal samples, Sniffles2 VCF SV files were processed through a somatic SV calling workflow with a threshold of 2 supporting reads for SV detection. A variant had to be present in 11% of the reads to be considered a somatic variant.
The SNF files were merged.
SVs for the normal, polyp, and adenocarcinoma samples were extracted using the SUPP_VEC function for BCFtools.
In-depth analysis of specific SVs unique to the adenocarcinoma sample was conducted by visualizing loci with Integrative Genomics Viewer (IGV).
Acknowledgements
The protocol was designed and utilized by Graham Scott Erwin and Katherine Wang