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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
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[Bug]: chrX coding #22

Closed epzjlm closed 1 month ago

epzjlm commented 2 months ago

Contact Details

No response

Scripts

02a-snp_data.sh, 03g-perform_positive_control.sh

What happened?

In 02a-snp_data.sh: I changed " --chr 1-23 \" to "--allow-extra-chr --chr-set 23 \". Fixed the X coding problem

03g-perform_positive_control.sh add --allow-extra-chr --chr-set 23 \ for plink2 before plot_GWAS.R

How can the bug be reproduced?

No response

R version

4.4.0 (April, 2024)

Python version

None

Relevant log output

No response