Virmid mutation calling, error
Entering edit mode
5.1 years ago
Chirag Nepal ★ 2.3k

I am trying Virmid (mutation calling tool)

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(
    at virmid.Virmid.main(

Similar error has been posted on sourceforge, but no good answer.

Has anyone encountered and solved this issue. Thanks !

Virmid Mutation • 913 views

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