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A definitive answer on running MuTect in STD mode? For a panel of normals or a single tumour sample.
Hi, I refer to the discussions on these posts:
The answers on these two posts appear to disagree on whether it is or isn't possible to run MuTect against multiple normal samples. In addition, it appears from another previous post
(http://gatkforums.broadinstitute.org/discussion/2432/mutect-in-high-confidence-hc-mode) that the correct way to run MuTect on "normal" samples is to disable all filters using the flag "--artifact_detection_mode". However, the first two links do not seem to reflect this requirement. And nowhere on the internet can I find any documentation to support the use of the "--normal_panel" flag as suggested by kcibul to specify the 'panel of normals' vcf needed to run in the HC+PON mode.
Finally, the original CGA documentation for MuTect specifies that when running the command for a tumour-normal pair, the order of the BAM files specified in the command is positional (i.e. that the normal BAM should go before the tumour BAM). This seems incompatible with running either multiple normal samples, or running a single tumour sample.
I have unsuccessfully scoured the internet for hours to get a definitive answer on how the correct way run MuTect to (a) generate a panel of normals and (b) analyse a single tumour sample (unpaired). It would be terrific if you could post a definitive example of the full command required to achieve these two objectives.
Telethon Kids Institute, Perth, Australia