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I posted the following message in this discuss http://gatkforums.broadinstitute.org/discussion/comment/16107/ but it seems that it might have slipped off the radar. I thought perhaps I should start a new one. Thank you.
Not sure if I have done something wrong here. After downloading version 3.1 from the github, I followed the instruction above (mvn verify -P!queue) to build it. However, when I ran the command below to check the version, it showed a much earlier one:
$ java -jar target/GenomeAnalysisTK.jar --version
Note that I have java 1.7 and I have not set up the IntelliJ.
I was given some vcf files created with version3.1 and I'll like to do some comparison works. Thank you.
PS: Just downloaded the version 3.2 source and compiled it. It also shows the same version 1.2-48-g442d33b