Question: Using AnnotSV to annotate XHMM output
0
gravatar for domzimm888
4 months ago by
domzimm8880
domzimm8880 wrote:

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

cnv xhmm annotsv annotation • 188 views
ADD COMMENTlink modified 9 days ago by LGMgeo90 • written 4 months ago by domzimm8880
0
gravatar for LGMgeo
9 days ago by
LGMgeo90
European Union
LGMgeo90 wrote:

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/bin

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

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

ADD COMMENTlink written 9 days ago by LGMgeo90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 710 users visited in the last hour