Usage information

Basic execution

This pipeline is configured to run on the IKMB MedCluster.

To execute, do:

nextflow run ikmb/vcf2ethnicity --vcfs '/path/to/*vcf.gz'

This options points to one or several VCF files (compressed bgzip). Each file is assumed to be accompanied by a matching index file (.tbi).

This option allows you to specify the desired analysis tool chain(s). Valid choices are:

These can be provided like so:

nextflow run ikmb/vcf2ethnicity --tools 'fastngsadmix,admixture' --vcfs '/path/to/*.vcf.gz'

We recommend to use fastNGSadmix only, since the overall runtime is much shorter and results are likely to be equivalent between the tools.