Pipeline for Illumina GSAv3 in Beagle, ADMIXTURE and qpAdm?

Question

[Leandro]

Hi,

I am working with human genotyping using Illumina GSAv3 BeadChip. I use GenomeStudio to convert the idat files and then save them with PLINK plugin. My question is, is there any pipeline to solve problems in PLINK files generated this way so that they are compatible with analyses such as imputation with Beagle and population structure with ADMIXTURE and qpAdm?

Answer 1

[barslmn]

You can directly output to VCF files using the Dragen array. https://help.dragenarray.illumina.com/

Contrary to what the name suggests you don't need a Dragen to run and, plain old CPU is enough.

I have an example pipeline here: https://github.com/gen-era/canvas-pipeline/blob/master/main.nf