Exome sequencing and targeted capture sequencing

 

In the SVA annotation and analysis. one has an option to only include genomic regions that are targeted by an exome sequencing or by a targeted capture sequencing.

(1) To use this option, you first need to prepare a text input file like this :

1 12345 22345
1 23456 33456
2 12345 22345
2 23456 33456

This file has three columns: [chromosome] [start_captured_region] [end_of_the_region]. These columns can be separated by either space or tab.

In most cases, this file is directly available from the manufacturer who provides the exome or targeted capture sequencing assay.

For this purpose, SVA also accepts [chromosome] column in format chr1 or CHR1.

Save this file to a file, say /DIR1/DIR2/DIR3/MyCaptured.txt.

(2) Add this line to your .gsap project file:

[CAPTUREDREGION]=/DIR1/DIR2/DIR3/MyCaptured.txt

Please include the full canonical path (starting with a '/' ) of the file.

 

Please note this option will include only the variants located within the genomic regions specified in this file in the following annotation and analysis procedures.