Variant Exporter

The Variant Exporter is a useful tool for verifying results received from one of STARInsight's analysis apps like Principal Component Analysis. We use the exporter internally for this purpose, and figured that our customers might find it useful, too.

Begin by clicking the Variant Exporter tile in the Apps page. 

You'll be prompted to select an analysis set and filter set from among those you have already created. This app is designed to perform QC on relatively small amounts of data. A good guideline is to use an analysis set and filter set combination which sums to a matrix of fewer than 150,000 values: 60 positions across 2500 samples, 100,000 positions across 15 samples, etc. 

The Variant Exporter outputs an Excel file containing several tabs. Each of those tabs is described below. If you would prefer a simplified result report containing only genotype values, click the "genotype only" option on the launch modal.

When your variant exporter job completes, open the report and download the full results file.

This results file is available as an Excel file with several tabs.

Summary = simply lists the number of samples and variant positions included in the analysis.

Variants = a list of all variant positions covered by the filter set for which variants were detected for any of the samples in the analysis set.

Genotype = a table where the X axis is each variant position (Chromosome | Position) and the Y axis is each sample, and the cells are genotype values for these positions (0/0, 0/1, 2/2, etc.) Note that STARInsight supports the storage of phased data (e.g., "1|0") where that information is present in the underlying VCF file ingested into the product. Imputed positions will be listed as {0|0}.

Quality Score = a table where the X axis is each variant position (Chromosome | Position) and the Y axis is each sample, and the cells are quality score values for each of these positions.

Read Depth = a table where the X axis is each variant position (Chromosome | Position) and the Y axis is each sample, and the cells are the read depth values for each of these positions.

Imputed = a table where the X axis is each variant position (Chromosome | Position) and the Y axis is each sample, and the cells indicate whether these positions have been imputed or not. An "f" character indicates a variant which has not been imputed. A {t} character indicates a variant which has been imputed. see Pre-Processing article for more information on imputation.

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