Genotype cluster plots format
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The genotype cluster plot data files contain genotype intensities per variant for a subset of samples.
The subset of samples is selected so that from each separate genotyping batch a maximum of 100 samples is chosen from each call category (AA/homozygous ref; Aa/heterozygous; aa/homozygous alt).
Genotypes with a missing call are all selected. The columns of the data file are explained below.
Column
Description
ID
Sample ID
batch
Genotyping batch
sex
Sample sex
intensity_ref
Reference allele intensity
intensity_alt
Alternative allele intensity
raw_call
Genotype call from chip
imputed_call
Genotype call after imputation
excluded
Whether sample was excluded from imputation (1=yes, 0=no)
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