Sex mismatch
Determine if a sample's predicted and known sex mismatch.
This tool uses read coverage data on the Y chromosome to predict the sex for a sample, and then the compares the prediction to the expected sex to see if there is a mismatch. The metric requires the extracted coverage information from running the extract
tool with the --bed
flag supplied.
How to run the tool
You can run this tool with one or more samples. At a minimum, the two required inputs are the list of sample names and the database (biometrics will automatically load all sample data from the database). Below is an example command:
You can also indicate your input samples via a CSV file, which has the same format as what you provided to the extraction tool, but you only need the sample_name
column:
Output
All analyses output a CSV file containing the metrics for each sample. It will be saved either to the current working directory or to a folder you specify via --outdir
. The table below describes each column in the CSV output.
Column Name | Description |
sample_name | Sample name. |
expected_sex | The sample's expected sex. |
predicted_sex | The sample's predicted sex. |
sex_mismatch | True if expected and predicted sex mismatch. |
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