qc_scripts/het_callrate.R
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Find heterozygosity and sample rate missingness outliers


qc_scripts/pcs_plot.R
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Code to plot the PCs to come up with an effective SD threshold to consier outliers


qc_scripts/ancestry_outliers.R
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Code to find ancestry outliers


genetic_qc.sh
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This is the code to perform the genetic QC at the sample and genetic level