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. There are three ways you can provide the input to the --input flag:

Method 1

You can provide the sample names. This assumes there is a file named {sample_name}.pk in the database directory.

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

Method 2

You can directly provide it the python pickle file that was outputted from the extract tool.

biometrics sexmismatch \
  -i /path/to/extract/output/C-48665L-N001-d.pk \
  -i /path/to/extract/output/C-PCYP90-N001-d.pk \
  -i /path/to/extract/output/C-MH6AL9-N001-d.pk \

Method 3

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.