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NCI-CGR
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TypeSeqHPV
NCI CGR laboratory HPV typing analysis workflows
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NCI-CGR/TypeSeqHPV Issues
Mia testing
Closed
4 years ago
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1
Mia testing #2
Closed
4 years ago
freq_matrix_results - need to add a minimum depth filter to this, so that the freq doesn't display if it didn't pass minimum requirements (otherwise the freq can be misleading); so for this, before the matrix is generated, if a frequency could be overwritten with "neg" if it didn't pass the filtering criteria that already in place (this is the "status" column in the "target_variant_results" file);
Closed
4 years ago
control_results - this code currently works correctly to create pass/fail results for the controls in a batch; currently only assesses for minimum coverage; need to make it possible to define each control as a positive or negative control, so for a positive control the requirement is to exceed the minimum reads specified, and for negative controls the requirement is to be less than the maximum reads specified; for this we need another column in the control definitions file called "control_type" or something, that will either have "positive" or "negative" for each control, so that they can each be assessed for pass/fail correctly; see email about this 2/2/2020
Closed
4 years ago