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difference between Mutect 1.1.7 and MuTect2
I am trying to detect somatic Snps in a normal/tumour pair. I tried MuTect2 under Gatk (java -jar GenomeAnalysisTK.jar -T MuTect2) and varscan 2. To my surprise, there was very little overlap between the predictions ( < 1%). In a paper, varscan2 and mutect had more in common but the paper had tested the stand alone mutect (mutect 1.1.4). I tried that but it wasnt compatible with my java7 environment so I tried stand alone mutect 1.1.7 instead (java -Xmx2g -jar mutect-1.1.7.jar --analysis_type MuTect).
To my surprise, there is still a big difference between the "Pass" predictions of Mutect2 and the "Keep" predictions of mutect 1.1.7 which are also very different from varscan2... Is this normal? What do I trust?
I certainly expected more overlap...