Virmid mutation calling, error
0
0
Entering edit mode
6.2 years ago
Chirag Nepal ★ 2.4k

I am trying Virmid (mutation calling tool) https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-8-r90 https://sourceforge.net/projects/virmid/

The tools predicts purity of samples and then calls somatic mutation

I ran the tools, it seems to run fine, as it predicts purity, but it gives an error before it produces the SNV list

I tried using two commands,

 java -Xmx4g -jar Virmid.jar -R $assembly -D Tumor.bam  -N Germline.bam
 -t 4 -q 20 -o Out2 -f


 java -Xmx4g -jar Virmid.jar -R $assembly -D Tumor.bam  -N Germline.bam
 -t 4 -q 20 -c1 10 -C1 500 -c2 10 -C2 500 -o Out2 -f

Error message

Exception in thread "main" java.lang.NullPointerException
    at virmid.Param.reportFile(Param.java:174)
    at virmid.Virmid.main(Virmid.java:129)

Similar error has been posted on sourceforge, but no good answer. https://sourceforge.net/p/virmid/discussion/general/thread/fd7aa4df/

Has anyone encountered and solved this issue. Thanks !

Virmid Mutation • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 2523 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6