fast-ngs-admix

This Nextflow pipeline estimates ancestry/admixture proportions of 23andMe files using the tools fastNGSadmix & iAdmix

Quick Start

The tool(s) can be run on:

• the command line
• Deploit (recommended)

Running on the command line

Dependencies

Nextflow Docker

An example run of the pipeline on the command line may look like this:

nextflow run lifebit-ai/fast-ngs-admix --genotypes_path s3://lifebit-featured-datasets/modules/ancestry/uk35C650_20170608144013.txt

The only required parameter is a 23andMe file, specified using the genotypes_path parameter. This can be a single 23andMe file or a folder conttaining 23andMe files.

Deploit

Deploit is a bioinformatics platform, developed by Lifebit, where you can run your analysis over the Cloud/AWS.

It is free for indivudal users to sign-up

You can run this pipeline under the modules section on the pipelines page, where this pipeline is named New ancestry. See an example job here including the output of the pipelines

Testdata

Testdata & reference files including the reference panel(s) are stored on the AWS S3 bucket s3://lifebit-featured-datasets/modules/ancestry/. This also includes an example 23andMe file.

Other Paramters

--fastngsadmix_fname reference panel for fastNGSadmix, default is refPanel_k27.txt

--fastngsadmux_nname Nname reference file fastNGSadmix, default is nInd_k27.txt

--iadmix_ref reference panel for iAdmix, default is k27.iadmix

--tool select with tool to run (fastngsadmix, iadmix or both), default is fastngsadmix,iadmix

--outdir directory to save results to, default is results