This document contains more info about QC step 11.

https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.shapiro.html https://vedexcel.com/how-to-perform-a-shapiro-wilk-test-in-python/

Here is a simple QC procedure we may want to consider that was used by
Megan and Camron in a recent paper  that I have attached.


Phenotypes were assessed for normality using the Shapiro–Wilk Test. Because
some of the data residuals devi- ated significantly from normality, we used
the orderNorm function to perform Ordered Quantile normalization43 on all
phenotypes.

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Rob

QTL analysis was performed in F2 mice using the R package R/qtl
(RRID:SCR_009085) as previously described.11,29,42 Quality checking
of genotypes and QTL analysis were performed in R (https://www.r-
project.org/) using R/bestNormalize (https://github.com/petersonR/
bestNormalize) and R/qtl.42 Phenotypes were assessed for normality
using the Shapiro–Wilk Test. Because some of the data residuals devi-
ated significantly from normality, we used the orderNorm function to
perform Ordered Quantile normalization43 on all phenotypes. QTL
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A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity