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mutations of Mutect2 gatk-18.104.22.168 are very different from gatk-3.0
We used mutect2 gatk-22.214.171.124 and compared results the older version 3.0 results with 16 samples, the filter results are different with older more than 90%. The raw results are more than 70% different.
Bam are the same.
where are differences between with the two versions?
Thank you !