> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v2/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/access-quality-control-v2/introduction/contamination.md).

# Contamination

Estimate sample contamination.

## Introduction

Two metrics are used to estimate sample contamination: minor contamination and major contamination. Moreover, minor contamination is calculated separately for collapsed and duplex BAMs. Both contamination metrics are produced by the `fingerprinting` SNP set. However, minor contamination is calculated using just the homozygous sites, whereas the major contamination is via the ratio of heterozygous to homozygous sites. For each contamination-BAM type combination there is a table showing per-sample contamination values and any associated metrics.

![Example MultiQC report showing fingerprinting results for 20 samples.](https://3106615528-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MbqIfOAQqfG2kMfi2uM%2Fsync%2Ffc12f25fc20fa917ec6d43adb084bf104ed5e8de.png?generation=1624566734236099\&alt=media)

## Methods

**Tool used:** [biometrics](https://github.com/msk-access/biometrics)\
 **BAM type:** (1) collapsed BAM and (2) duplex BAM\
 **Regions:** MSK-ACCESS-v1\_0-curatedSNPs.vcf

It is a two step process to produce the table: (1) extract SNP genotypes from each sample using `biometrics extract` command and (2) perform a pairwise comparison of all samples to determine sample relatedness using the `biometrics minor` and `biometrics major` commands. Please see the biometrics documentation for further documentation on the methods.

## Interpretation

### Minor contamination

Samples with minor contamination rates of >0.002 are considered contamination.

### Major contamination

The fraction of heterozygous positions should be around 0.5. If the fraction is greater than 0.6, it is considered to have major contamination.