Genotype_QC_figures

Missingness

## `summarise()` ungrouping output (override with `.groups` argument)

MAF

Hardy Weinberg Equilibrium

Relatedness

shiny::includeHTML(relatedness_path)

Sample to Sample Relatedness

Scale by shared-sites

X Axis

Shared hets Shared hom-alts Homozygous concordance Relatedness IBS0 IBS2

Y Axis

Shared hets Shared hom-alts Homozygous concordance Relatedness IBS0 IBS2

Sample Depth Metrics

X Axis

Mean depth of genotyped sites Mean depth of all sites Mean allele balance % reads with neither REF nor ALT Number of 0/0 sites Number of 0/1 sites Number of 1/1 sites Number of unknown sites Number of known sites Proportion sites with AB < 0.1 or AB > 0.9 Scaled mean depth on X Number of 0/0 sites on X Number of 0/1 sites on X Number of 1/1 sites on X Scaled mean depth on Y

Y Axis

Mean depth of genotyped sites Mean depth of all sites Mean allele balance % reads with neither REF nor ALT Number of 0/0 sites Number of 0/1 sites Number of 1/1 sites Number of unknown sites Number of known sites Proportion sites with AB < 0.1 or AB > 0.9 Scaled mean depth on X Number of 0/0 sites on X Number of 0/1 sites on X Number of 1/1 sites on X Scaled mean depth on Y

Choose pre-set selection for sample plot:

• Sex QC: Number of 0/1 sites on X vs scaled mean depth on chrX
• Sex ploidy QC: Scaled mean depth on chrX vs. chrY
• General QC: number of sites with unknown genotype vs. proportion of hets with allele balance outside of 0.1 - 0.9
• Depth and allele QC: mean depth vs. mean het allele-balance

Ancestry

shiny::includeHTML(ancestry_path)

Ancestry Prediction

X Axis

Y Axis