This is a snakemake pipeline for aligning cattle Oxford Nanopore data to two cattle genome assembiles (ARS-UCD1.2 and UOA_Angus) using minimap2 and ngmlr and calling structural variants using different sv callers. The output is the high confidance sv set.
aligners: ngmlr minimap2
sv callers: svim pbsv sniffles
others: survivor bcftools samtools vep
Conda environment files containing the some dependencies can be found in the envs directory. These can be automatically installed and managed by providing the --use-conda argument to snakemake: snakemake --use-conda ....
