Export Text Files and Charts

In addition to sample reports, BaseSpace VariantStudio provides tools for exporting to text files and graphical representations of data.

Export Data Files

Exporting filtered variants and all transcripts for variants generates a tab-separated values file. Exporting filter history generates a comma-separated values (CSV) file. These text file formats are not application-specific and can be opened in any text editor. The ANT file is a binary file that contains

Command

Filtered Variants

(TSV)

Description

Exports filtered variants from the current sample.

For variants that overlap multiple genes, only the transcripts that appear on the interface are exported.

Exports all transcripts for filtered variants in the sample.

All Transcripts for

Variants (TSV)

Filter History (CSV) Exports a report of all filters applied to the project.

Export Charts

From the Charts menu, select a preferred format to export results in a histogram or a pie chart.

Command

Histogram

Pie Chart

Description

Generates a histogram of filtered results from the Variants table.

• Use the Plot drop-down list on the generated histogram

(

Figure 38 ) to represent variant quality values or indel

variant length.

• Use Data Source options to show all variants or only filtered variants.

Generates a pie chart of filtered results from the Variants table.

• Use the Plot drop-down list on the generated pie chart

(

Figure 39 ) to represent percentages of variant call filters,

variant type, genotype, coding regions, or filtered variants.

• Use Data Source options to show all variants or only filtered variants.

From the generated chart, click Copy to Clipboard to transfer the image from the BaseSpace

VariantStudio software to an application that supports images.

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Figure 38 Histogram

Figure 39 Pie Chart

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Appendix A  Annotation Sources

Annotation Sources

Annotation Sources 66

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