Variant Discovery    ◾    147

Assuming that your VCF file is in the current directory, you can run the following on the

command line:

java -jar SIFT4G_Annotator.jar \

-c -i humanSNP.vcf \

-d GRCh38.78 \

-r output -t

The option “-jar” for the SIFT 4G path, “-c” is essential for the command line, “-i” for the

input path, “-d” for the database path, “-r” specifies the output folder, and “-t” is to extract

annotations for multiple transcripts.

The above command generates two files: an Excel annotation file with “.xls” file exten-

sion and a VCF file.

Instead of the command line, you can also use SIFT 4G with a graphic user interface

(GUI) by running the following command:

java -jar SIFT4G_Annotator.jar

This will open SIFT interface where you can browse to select the VCF file and the database

and click Start to annotate the variants. The links of the two output files are given at the

bottom of the GUI (Figure 4.9).

We can open the Excel file to check its content (Figure 4.10). We can notice that some

annotations have been added to the variants, such as Ensemble transcript ID, gene ID,

gene name, region, variant type (synonymous or nonsynonymous), SIFT score, median

FIGURE 4.9  SIFT 4G annotator.