Genotype cluster plots format
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) |
Read more about cluster plots.
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