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The legacy workflow prunes sets of subjects using IBS/IBD and Call Rate [1]. These related subjects are removed prior to running PCA [2] and HWE [3]. There is some discussion about doing this in different ways (#10) but here I just want to replicate the legacy process. Unfortunately, testing is going to be difficult because the current test data does not contain any related sample/subject (#2).
Action Items
Create a list of related subjects using IBS/IBD and Call Rate (i.e., refactor [1])
Create a rule to filter these subjects and plug them into the PCA (MAF+LD) and HWE (MAF+Autosome+SNPs) filter process.
The legacy workflow prunes sets of subjects using IBS/IBD and Call Rate [1]. These related subjects are removed prior to running PCA [2] and HWE [3]. There is some discussion about doing this in different ways (#10) but here I just want to replicate the legacy process. Unfortunately, testing is going to be difficult because the current test data does not contain any related sample/subject (#2).
Action Items
Links
GwasQcPipeline/modules/Snakefile_remove_related
Lines 3 to 10 in 1d15a35
GwasQcPipeline/modules/Snakefile_pca
Lines 28 to 34 in 1d15a35
GwasQcPipeline/modules/Snakefile_HWP
Lines 33 to 39 in 1d15a35
Related
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