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Test-drive the GATK tools and Best Practices pipelines on Terra
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MuTect2 Empty vcf file even with tumor/normal pair input
Hi I am aware of a bug in MuTect2 that gives an empty vcf file when generating PON. However I am experiencing the same issue when using tumor/normal pair mode as well. The log file indicates a "Ran local assembly on 0 active regions" error. The only different aspect of my dataset is that I am looking at only 3 amplicons on three different locations in human. Does this have an impact of how MuTect2 works?