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I have been running gatk (v version 1.4-17-gd5199db)) with java 1.7.0
I have been running gatk (v version 1.4-17-gd5199db)) with java 1.7.0 and all seems well. In fact, running with previous java version (early 1.6 I think), was not working properly ...eg skipping chromosomes in realignment etc. As you say gatk not supporting java 1.7 is there something that I am missing. Is it just functionality of some walkers etc that require java 1.6 or are my processed bams not going to be complete eg not infact realigning pr recalibrating effectively under java 1.7? . No warnings arising or chromosome skipping etc. Or this this particular to the version GATK i am running. I was about to upgade gatk but want to get java right first.
Thank you for your help.