BaseSpace VariantStudio User Guide

Annotate Variants

From the Annotations and Classification tab, use commands on the Annotate menu to annotate variants in the current sample with options to annotate all variants or only those variants specified. All coordinates used in BaseSpace VariantStudio are genomic coordinates on the positive strand.

Always annotate variants before applying filters.

NOTE

An internet connection is required to annotate variants. After annotating, an internet connection is not necessary.

Figure 13 Annotate Menu

Command

Annotate

Custom Annotation

Custom Gene

Annotation

Description

Annotates variants in the project using the following options:

• All Variants of Current Sample—Annotates all variants in the current sample. The current sample is listed in the

Current Sample field of the Samples menu.

• Exonic Variants of Current Sample—Annotates variants found within an exon plus 20 bp on either side of the exonic region to include the annotation of splice site variants.

• Selected Variants of Current Sample—Annotates only the variants that you have selected or filtered.

• All Samples—Annotates all variants within each sample imported into the project. This process can take time to complete depending on the number of samples in the project.

Opens a window to browse to the location of the custom annotations file for variant-level annotation. For more information, see

Input File for Custom Variant Annotations on page 29 .

Opens a window to browse to the location of the custom annotations file for gene-level annotation. For more information, see

Input File for Custom Gene Annotations on page 29 .

Opens a window that lists the default transcript for each gene and options for changing to other than the default transcript.

Set Default

Transcripts

NOTE

Although mitochondrial variants can be imported, the annotation database does not provide annotations for these variants.

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Annotation Options

From the Annotate menu, click Annotation Options. The Annotation Options form opens with options to annotate only certain variants.

Figure 14 Variant Option Form

Option

Transcript Annotation

Transcript Source

Type

Forget BaseSpace

Logon

Description

Provides options to annotate only variants in the canonical transcript, which is the longest translated transcript in the gene, and variants in intronic regions.

Annotates variants identified in a specific annotation source, which is RefSeq, by default.

The default can be changed to Ensembl by editing the mode entry in the BaseSpace VariantStudio configuration file

(VariantStudio.exe.config), as follows:

<add key="Mode" value="Ensembl"/>

Close and reopen BaseSpace VariantStudio to enable the change.

Clears BaseSpace login information, such as ID and password.

Set Default Transcripts

1 Click Set Default Transcripts. A window opens that lists the default transcript for each gene. By default, BaseSpace VariantStudio lists the canonical transcript, which is the longest translated transcript in the gene.

2 For genes with multiple transcripts, use the drop-down list to set the default to another transcript.

BaseSpace VariantStudio v2.2 Software User Guide

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Figure 15 Set Default Transcripts

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Alternatively, click Browse to navigate to a tab-delimited text file containing your preferred default transcripts and click Load.

Input File for Default Transcripts

The input file for default transcripts requires two columns: Gene_Name and Transcript_

Name, as shown in the following example.

Gene_Name

ACTN3

ADH1B

AKAP10

Transcript_Name

NM_003793.3

NM_000668.4

NM_007202.3

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