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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 #57

Open epzjlm opened 2 weeks ago

epzjlm commented 2 weeks ago

Contact Details

No response

Scripts

02a-snp_data.sh, 04a-convert_snp_format.sh

What happened?

PLINK2 recodes 23 to X. This results that chrX doesn't match to reference file in easyQC in 02a and also not in 04.

How can the bug be reproduced?

script04a bug

R version

4.4.0 (April, 2024)

Python version

None

Relevant log output

No response