This is a Snakemake pipeline designed to take Oxford Nanopore Technologies data from fastq's to variant calls. In additions to traditional SNVs and indels, this pipeline will also call methylation using nanopolish.
The Snakefile is under workflow.
The functions performed by this tool are as follows:
- minimap2
- Sniffles
- CuteSV
- SVIM
- Clair3
- longphase
- In-house pipeline
There are dummy rules which can be added to the snakemake command which run specific tests. They are listed below:
- all_align
- Runs minimap2 for all samples
- all_sv
- Runs all SV callers for all samples
- all_snv
- Runs Clair3 for all samples
- all_haplotag
- Runs haplotype phasing using longphase for all samples
- all_haplotag_methyl
- Haplotags bams and links methylation bams for all samples
- all_minimap_methyl
- Links methylation to unphased bams for all samples