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Update Input_POGENOM_Usage.rst
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andand authored Apr 27, 2021
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4 changes: 1 addition & 3 deletions docs/source/Input_POGENOM_Usage.rst
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Expand Up @@ -102,9 +102,7 @@ In the "Input_POGENOM_config.json" file, set the parameters to be used. It conta
It cannot be empty.

"subsample": "TRUE",
Sample/genome combinations above used-defined threshold (i.e., min_cov, Breadth) will be, by default (``"TRUE"``), downsampled to user-defined Minimum median coverage.
If the user do not want to downsample the selected Sample/genome combinations, set option to ``"FALSE"``.
It cannot be empty.
Sample/genome combinations fulfilling the user-defined thresholds (i.e., min_coverage, min_breadth) will, per default (``"TRUE"``), be downsampled to the user-defined min_coverage median coverage. If the user do not want to downsample, set option to ``"FALSE"``. It cannot be empty.

"min_bsq_for_cov_median_calculation": 15,
Minimum base quality when counting the coverage depth per genome position during coverage calculation. Integer. It cannot be empty.
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