> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/biometrics/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/biometrics/develop-2/sex-mismatch.md).

# 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. |