Impute vcf files / snp chip array

[LouisLeNezet]

Description of feature

For the next release (not the first one) it would be nice to be able to impute SNP chip array data.
To do so, new software would be necessary (beagle5, impute5, ...).
We would also need to be able to simulate such data from the localisation of the SNPs used in a given array.

[smlmbrt]

Is this any closer? Or do you know other pipelines that might work in this way?

[LouisLeNezet]

Hi !
This is planned, but no due date for the moment as I currently have a lot of other work to do.
The plan is to collaborate with the imputation server of Michigan and convert what they've done in nf-core.

[LouisLeNezet]

Here is a list of what to do

• nf-core modules to add
  • minimac4 #7759
  • beagle
  • eagle #7760
  • impute5
• subworkflows to create
  • phasing using eagle
  • phasing using bealge
  • imputation using minimac4
  • imputation using impute5