Aggregate Genotypes of Interest Report
If the genotypes of interest feature is turned on, the app produces a downloadable CSV file (*.aggregate.genotype.csv). This file summarizes the genotypes of all the samples in the current run. Each row in the file represents a position in the input genotypes of interest (GoI) VCF files. The positions are sorted by genomic coordinate. To download the aggregate genotypes of interest report, select Export (CSV) from the Aggregate Summary page.
|
Statistic |
Definition |
|---|---|
|
Chr |
Name of reference chromosome. |
|
Position |
Position within reference chromosome. |
|
ID |
Variant identifier obtained from the ID column of the genotype.csv file of the first sample. For positions in the GoI input VCF files |
|
RefAllele |
The reference allele. |
|
AltAllele |
The alt allele. |
|
GoIFileName |
The name of the input genotypes of interest (GoI) VCF file. If multiple GoI files contain the same variant, the first GoI file name is used. |
The file also contains N additional data columns (N is the number of samples in the run). Each data column contains the genotypes of a sample (the header is the sample name). The genotypes are obtained from the genotype.csv file (column GenotypeForwardAlleles) for each underlying sample. The sample order depends on the order of the app results and can vary from analysis to analysis.