Update branch #311
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Update branch #311
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…ci call rate filters
switch snp and call rate filters
The `QC_Report.xlsx` was missing data for the `is_unexpected_replicate` column in the `SAMPLE_QC`, `SAMPLE_CONCORDANCE`, and `SUBJECT_QC` sheets. This issue arose from a column name change in commit `825c8a57e2003e8c5a55aded8759584f950752cc`, where `Unexpected Replicate` was renamed to `is_unexpected_replicate`. The renaming caused blank entries due to the reindexing step in `qc_report_tables.py`. During reindexing, `is_unexpected_replicate` was not found in the DataFrame because of the earlier renaming, leading to NaN values. Pandas docs state, "By default, values in the new index that do not have corresponding records in the DataFrame are assigned NaN." To resolve this, the column names have been reverted to their original title, `Unexpected Replicate`.
- Renamed parameter `sample_qc_csv` to `subject_qc_csv` to better reflect its intended use.
…s Removed" We noticed a discrepancy in the terminology we are using in Table 4a. It uses "Expected Duplicates Removed", while other parts of the pipeline uses "Expected Replicates". So we updated Table 4a to "Expected Replicates Removed" for consistency throughout the pipeline.
bugfix: `is_unexpected_replicate` data missing in `QC_Report.xlsx`
- Removed "IdatsInProjectDir" from _SAMPLE_QC_COLUMNS and QC_Report.xlsx. - The "IdatsInProjectDir" column was empty in QC_Report.xlsx because it is not present in sample_qc.csv. - The equivalent column "is_missing_idats" is already included in QC_Report.xlsx, containing the same information from cgr_sample_sheet.csv. - Therefore, the "IdatsInProjectDir" column has been removed to avoid redundancy.
Removes "Expected Replicate" from _SAMPLE_QC_COLUMNS and thus the QC_Report.xlsx. It duplicates the more informative "Replicate IDs" column in the QC_Report.xlsx
- Introduces functionality to calculate the total number of QC issues
present in a sample.
- Addresses missing data in the "Count_of_QC_Issue" column of
QC_Report.xlsx.
- Calculates the number of "TRUE" occurrences in five boolean columns:
"Low Call Rate",
"Contaminated",
"Expected Replicate Discordance",
"Unexpected Replicate",
and "Sex Discordant".
- Fills in missing data for "Sample Pass QC" column in QC_Report.xlsx.
- Populates the column with a boolean value indicating if a sample passed all QC metrics:
"Low Call Rate",
"Contaminated",
"Expected Replicate Discordance",
"Unexpected Replicate",
and "Sex Discordant".
- A sample passes QC if `Count_of_QC_Issue` is 0 (no QC issues).
- Otherwise, the sample fails and the column is set to False.
bugfix: retrieve additional missing data from `QC_Report.xlsx`
Issue 222
kliao12
merged commit 1dac0b3
into
302-skip-merging-graf-king-and-plink-results-to-make-the-qc-pipeline-more-efficient
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