# Minor contamination

Minor contamination is a metric to see if a sample is contaminated with small amounts of DNA from another unrelated sample. The metric requires the extracted pileup information from running the `extract` tool.

## 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 minor \
  -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 minor \
  -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 minor \
  -i samples.csv \
  -db /path/to/store/extract/output
```

## Output

All analyses output a CSV file containing the metrics for each sample. An interactive bar graph can also optionally be produced by supplying the `--plot` flag. These outputs are saved either to the current working directory or to a folder you specify via `--outdir`.

### CSV file

The CSV file contains metrics for each pair of samples compared (one per line). The table below describes each column in the CSV output:

| Column Name              | Description                                                        |
| ------------------------ | ------------------------------------------------------------------ |
| sample\_name             | Sample name.                                                       |
| sample\_group            | Sample group (if available).                                       |
| sample\_sex              | Sample sex (if available).                                         |
| sample\_type             | Sample type (if available).                                        |
| total\_homozygous\_sites | Total number of homozygous sites.                                  |
| n\_contributing\_sites   | Total number of contributing sites (i.e. those that have MAF > 0). |
| minor\_contamination     | Minor contamination metric.                                        |

### Interactive plot

Two interactive plots are produced that help you further investigate the data.

{% hint style="info" %}
The sample order is the same between the two plots.
{% endhint %}

{% hint style="info" %}
You can also control the minor contamination threshold (the horizontal red line) via the `--minor-threshold` flag.
{% endhint %}

#### Minor contamination plot

Shows the minor contamination for each sample, ranked from highest to lowest. You can hover over each bar to get more information about the sample.

![](https://1004483223-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MOgRqoKNYiKeu3KYvC1%2Fsync%2Fe082a5404e82e386fed8873f6016ce2b5e1ea0e2.png?generation=1615391554062483\&alt=media)

#### Contributing sites plot

Shows statistics for each site that contributes to the minor contamination calculation. Only sites with a minor allele frequency > 0 are shown. You can hover over each point to get more information about that site.

![](https://1004483223-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MOgRqoKNYiKeu3KYvC1%2Fsync%2F4073a53302341e1471853e563332957ddedf620e.png?generation=1615391556669456\&alt=media)

## Algorithm details

Minor contamination is calculated as the average minor allele frequency for homozygous sites. A homozygous site is defined as one with < 10% minor allele frequency.