Exporting Data from VarSeq

To export data from one or more tables in VarSeq, either click on the Export menu icon or go to File > Export. Currently, data can be exported in these formats:

  • Text File...: Export the data to a text file. The delimiter and sub-delimiter can be specified in the export dialog. Column headers and column group headers can also optionally be selected in the dialog. See Export to Text.
  • VCF File...: Export the data to a VCF file. See Export to VCF.
  • Annotation File...: This options exports the data into the Convert Wizard so an annotation source can be created from the data. See Annotation Convert Source Wizard for more information.
  • XLSX File...: Export the data to an Excel XLSX file. XLSX files are limited to 1,048,576 rows and 16,384 columns. See Export to Excel (XLSX).

Export to Text

Select Data To Export

Data from one visible table can be exported to a text file at a time. Select the table to export by clicking on it in the list if it is not already selected. See Text export select the table to export.

Note

If the table you would like to export is not listed, close this dialog and make sure the table is visible or in an open tab, view or window.

Text Export 1

Text export select the table to export

Set Export Parameters

In the next dialog select the column groups and columns to export to a text file (see Text export field selection dialog):

Text Export 2

Text export field selection dialog

In the next dialog there are several options for export (see Text export parameters dialog):

  • Include or exclude a header with an optional prefix.
  • Include or exclude the column group headers.
  • Set the text file delimiter (default is Tab \t).
  • Set the list delimiter (default is Comma ,).
  • Set the missing value symbol (default is Empty).
  • Select the samples to export if the project contains more than one sample. Options include: Current Sample, Affected Samples, or All Samples.
  • Set the file path.

When all of the parameters are set click Export.

Text Export 3

Text export parameters dialog

Note

If more than one sample is exported for the specified table, the table will be updated to include the variants for the sample as if the current sample was set to each sample manually before exporting the data.

Export Complete

When export is complete you can open the directory containing the files by clicking on Open Location on the last dialog.

Text Export 4

Text export progress dialog

Export to VCF

Select Data To Export

Data from one visible table can be exported to a VCF file at a time. Select the table to export by clicking on it in the list, if it is not already selected. See VCF export select the table to export.

Note

Only tables that contain variants will be selectable for VCF export. If the table you would like to export is not listed, close this dialog and make sure the table is visible or in an open tab, view or window.

VCF Export 1

VCF export select the table to export

Set Export Parameters

In the next dialog Select the column groups an columns to export to both INFO and FORMAT fields in the VCF file (see VCF export field selection dialog):

VCF Export 2

VCF export field selection dialog

On the next dialog there are several options to set (see VCF export parameters dialog):

  • Select the samples to export if the project contains more than one sample. Options include: Current Sample, Affected Samples, or All Samples.
  • Set the file path.

When all of the parameters are set click Export.

VCF Export 3

VCF export parameters dialog

Note

If more than one sample is exported for the specified table, the table will be updated to include the variants for the sample as if the current sample was set to each sample manually before exporting the data.

Export Complete

When export is complete you can open the directory containing the files by clicking on Open Location on the last dialog.

Text Export 4

Text export progress dialog

Export to Excel (XLSX)

Select Data To Export

Data from one or more visible tables can be exported to an Excel XLSX workbook. By default all visible tables are selected for export. To change the selection, click in the table selection dialog. <Shift> + Left-Click and <Ctrl> + Left-Click multiple selection options are available to select more than one table at a time. See Excel XLSX export select the tables to export.

Note

If the table you would like to export is not listed, close this dialog and make sure the table is visible or in an open tab, view or window.

XLSX Export 1

Excel XLSX export select the tables to export

Set Export Parameters

In the next dialog select the column groups and columns to export to an Excel XLSX file (see Excel XLSX export field selection)

XLSX Export 2

Excel XLSX export field selection

In the next dialog there are several options for export (see XLSX export parameters dialog):

  • Include or exclude tables to export.
  • Include or not hyperlinks in the Excel file.
  • Set missing value symbol (default is Empty).
  • Select the samples to export if the project contains more than one sample. Options include: Current Sample, Affected Samples, or All Samples.
  • Set the file path.
XLSX Export 3

XLSX export parameters dialog

Note

If more than one sample is exported for the specified table, the table will be updated to include the variants for the sample as if the current sample was set to each sample manually before exporting the data.

Export Complete

When export is complete you can open the directory containing the files by clicking on Open Location on the last dialog.

VCF Export 4

VCF export progress dialog