3.12.7. Importing Breakends

You can import complex rearrangements with breakends from vcf files. When imported, the rearrangements from these files will be available as a Breakend table that can use VarSeq’s annotating and filtering algorithms. To import breakends, you must already have variants imported into your project.

Select Files to Import

The import wizard will step you through all of the import options to bring breakend data into VarSeq.

The first step is to select the files to import.

Import Wizard Step 1

Select the files to import on the first step of the import wizard.

The next step is to associate the relationship between the files and samples.

Associating Inputs with Existing Samples

Each file selected for import must have the input data associated with a sample that already exists in the project. This is done by selecting the file from the dropdown list next to the corresponding sample that already exists in the project. If you are importing a vcf file which has multiple samples, the sample name from the file will appear after the file name in the dropdown list.

Associating Samples and Input Files

Selecting the file that corresponds to the sample that is already imported into the project.

After all of the samples and input files have been matched click the Next button move to the field behavior selection page.

Setting the Import Field Behavior

By default, all of the fields are imported and merged for each unique breakend. You can change the merge behavior to change how the field values are combined when there are multiple records at the sample location.

Changing the field merge behavior

Selecting the text input fields that correspond to the required genomic fields and CNV type field.

By default, all of the fields will be merged by creating a Unique list of values for the field across all samples and files, this will keep the field a variant site field. Other merge options include:

  • NumericMax: For integer, integer array, float or float array field types. Takes the maximum of all values for the field in all files.

  • NumericMin: For integer, integer array, float or float array field types. Takes the minimum of all values for the field in all files.

  • NumericMean: For integer, integer array, float or float array field types. Takes the mean of all values for the field in all files.

  • KeepMatching: For all field types. Only keep the value if all files that have a value for the specified field match.

  • TakeFirst: For all field types. Take the first value seen.

  • TakeAll: For all field types. Take all of the field values for all of the merged records and combine them in a list.

  • Sample: For all field types. This will take all of values for this field and make them sample specific based on the sample/input file association.

Fields can also be dropped from the import by unchecking the Select Field checkbox. Unchecked fields will not be read and imported into the project.

Import Summary

The final page of the import wizard is a summary of the import process. To finalize the import click Finished. This will import the text file into VarSeq. Please note that this may be completed in several steps.

Requirements

Requires that samples with variants have been imported.

Output

Creates a new table for the imported breakends.