Nanopore¶

To run vip with nanopore data, just specify nanopore as the sequencing_platform in your sample sheet. The other options for this field are "illumina" and "pacbio_hifi" and can be used in a similar manner.

Samplesheet¶

See an example for the samplesheet below, the example show the samplesheet for a run starting from the cram, but the 'sequencing_platform' can also be used to achieve the same for a run with the fastq workflow.

individual_id   sequencing_platform cram
your_sample_id  nanopore    path/to/your/nanopore.cram

Run the pipeline¶

cd vip
vip --workflow cram --input path/to/samplesheet.tsv --output path/to/output/folder

For an example on how to generate output for FASTQ files using the Oxford Nanopore platform see here.