search

genetics-of-dna-methylation-consortium / godmc_phase2

This repository contains the code to run the analysis pipeline for phase 2 of goDMC released June 2024.
GNU General Public License v3.0
2 stars 1 forks source link

[Code Refactor]: Any other option for `quality_type` in the config file if we use Sanger imputation server? #25

Closed SiyiSEA closed 1 month ago

SiyiSEA commented 1 month ago

Contact Details

s.w.wang@exeter.ac.uk

Path to affected file

config file.

Type of refactor

Code optimisation, Comment improvement

Description of required code refactor

Hi,

My data has been imputed by the Sanger Imputation Server which use the SHAPEIT2 + PBWT for phase and imputation.

Due to the output files from Sanger Imputation contain the INFO score, I set the quality_type = 'minimac' temporarily.

Any other better suggestion for setting the quality_type in the config file, since there is no choice fit the Sanger Imputation?

Thanks.

ejh243 commented 1 month ago

Searching the code base, this variable isn't actually used? Should we remove it therefore @epzjlm ?

epzjlm commented 1 month ago

Yes let's remove it.