Using AnnotSV to annotate XHMM output

Question

[domzimm888]

Hi all

I'm trying to annotate the .vcf output file with annotSV but I'm running into errors right from the start. I'm getting the error "'ANNOTSV' environment variable not specified. Please define it before running AnnotSV. Exit"

I'm running the command "$ANNOTSV/bin/AnnotSV -SVinputFile xhmm.vcf > AnnotSV.log"

Any help would be greatly appreciated.

Dom

Answer 1

[LGMgeo]

ANNOTSV is the environment variable defining the installation path of the software.

• In csh, you can define it with the following command line: setenv ANNOTSV /path_of_AnnotSV_installation

• In bash, you can define it with the following command line: Export ANNOTSV=/path_of_AnnotSV_installation

I advise you to save the good command in your .cshrc or .bashrc file.