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:

biometrics sexmismatch \
  -sn C-48665L-N001-d C-PCYP90-N001-d C-MH6AL9-N001-d \
  -db /path/to/store/extract/output

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:

biometrics sexmismatch \
  -i samples.csv \
  -db /path/to/store/extract/output

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.