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Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. #7261

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Jun 11, 2021
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Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. #7261

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2 changes: 1 addition & 1 deletion scripts/gatkcondaenv.yml.template
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Expand Up @@ -38,7 +38,7 @@ dependencies:
# if you wish to update, note that versions of conda-forge::keras after 2.2.5
# undesirably set the environment variable KERAS_BACKEND = theano by default
- defaults::intel-openmp=2019.4
- conda-forge::scikit-learn=0.22.2
- conda-forge::scikit-learn=0.23.1
- conda-forge::matplotlib=3.2.1
- conda-forge::pandas=1.0.3

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3 changes: 1 addition & 2 deletions src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py
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Expand Up @@ -786,8 +786,7 @@ def __init__(self,
# the expected number of erroneously mapped reads
mean_mapping_error_correction_s = eps_mapping * read_depth_s * shared_workspace.average_ploidy_s

denoised_copy_ratio_st = ((shared_workspace.n_st - mean_mapping_error_correction_s.dimshuffle(0, 'x'))
/ ((1.0 - eps_mapping) * read_depth_s.dimshuffle(0, 'x') * bias_st))
denoised_copy_ratio_st = shared_workspace.n_st / (read_depth_s.dimshuffle(0, 'x') * bias_st)
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I feel like this change should have broken a test, but it looks like the only tests test the Python environment. Should we add tests (maybe not for this PR)?


Deterministic(name='denoised_copy_ratio_st', var=denoised_copy_ratio_st)

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2 changes: 1 addition & 1 deletion ...est/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java
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Expand Up @@ -25,7 +25,7 @@ public Object[][] getDataPackagePresent() {
{ "pymc3", "3.1" },
{ "keras", "2.2.4" },
{ "h5py", "2.10.0" },
{ "sklearn", "0.22.2.post1" },
{ "sklearn", "0.23.1" },
{ "matplotlib", "3.2.1" },
{ "pandas", "1.0.3" },
{ "argparse", null },
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