Minor contamination

Calculate 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.

The sample order is the same between the two plots.

You can also control the minor contamination threshold (the horizontal red line) via the --minor-threshold flag.

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.

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.

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.