> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v1/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-v1/duplex-minor-contamination.md).

# Duplex Minor Contamination

![](https://2763969089-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M52gq1rRSDQOKMQGEuR%2F-MA6eOoGa8fgZks5LAFP%2F-MA6ebzjOIwoD_5DhYRj%2FScreen%20Shot%202020-06-18%20at%209.42.11%20AM.png?alt=media\&token=7e34e3b2-15ff-4499-a98e-33bb6c362cab)

**Theoretical Method**

Minor contamination from duplex bams for tumor sample (identified by the title file) is additionally checked. This analysis is done using the same fingerprint SNP in identified in the FP\_configuration file although there is a 200x coverage threshold. 

{% hint style="info" %}
This 200x coverage threshold essential limits the analysis to the 31 specfically designed FP\_SNPs.
{% endhint %}

The Minor Contamination Rate is the average (mean) minor allele frequency from homozygous fingerprint SNPs, where homozygous sites as those harboring < 5% minor allele frequency in the sequence data.

{% hint style="info" %}
These calculations were done using duplex bams. Allele counts are measured from waltz pileups from Pool A and B
{% endhint %}

**Technical Methods**

* Tool Used:
  * Waltz PileupMetrics
  * fingerprinting.py
* Input
  * output\_dir : Directory to write the Output files to
  * waltz\_dir\_A: Directory with waltz pileup files for target set A
  * waltz\_dir\_B: Directory with waltz pileup files for target set B
  * waltz\_dir\_A\_duplex: Directory with waltz pileup files for Duplex target set A
  * waltz\_dir\_B\_duplex: Directory with waltz pileup files for Duplex target set B
  * fp\_config: File with information about the SNPs for analysis (MSK-ACCESS-v1\_0-TilingaAndFpSNPs.txt)
  * title\_file: Title File for the run
* Output
  * FPResults/minorDuplex Contamination.txt
  * MinorDuplexContaminationRate.pdf

**Interpretations**

Samples with Duplex Minor contamination rates of >0.002 are considered contamination.