search

NCI-CGR / GwasQcPipeline

The CGR GWAS QC processing workflow.
https://nci-cgr.github.io/GwasQcPipeline/
MIT License
0 stars 3 forks source link

skip merging Graf, King and Plink results to make the QC pipeline more efficient #302

Closed shukwong closed 2 months ago

shukwong commented 4 months ago

currently, the step (sample_concordance_summary?) takes >24 hours for 90k sample QC run because it needs to merge Graf, King, and Plink results. Graf and King relatedness results are not used downstream. We could skip merging these results. The Plink results will still be needed to estimate duplicates and close relatives.

carynwillis commented 4 months ago

For all sample sizes, we will instead output the Graf and King results separately instead of merging them with the Plink results.