> 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/contributing-sites-for-noise.md).

# Contributing Sites for Noise

Understanding how many individual positions lead to noise in the duplex bam

![](https://2763969089-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M52gq1rRSDQOKMQGEuR%2F-M9Z39Nd7c6cJRknLQBm%2F-M9Z7BBqxIodtN6YseQ_%2FScreen%20Shot%202020-06-11%20at%2012.05.02%20PM.png?alt=media\&token=f8da26f9-18fd-40c7-bc31-3c427a888509)

**Theoretical Method**

Count the number of positions in the bam that have an alt allele frequency of >0 and <2%

{% hint style="info" %}
Note: Duplex bams are used for this calculation, and only substitutions are included, not insertions or deletions
{% endhint %}

**Technical Methods**

* Tool Used:
  * Marianas
  * Waltz PileupMetrics
  * calculate\_noise.sh (script aggregates across samples from Waltz folder)
* Input
  * sample\_id-duplex-pileup.txt (for duplex noise calculation)
* Output
  * noise.txt

**Interpretations**

For the most accurate results, we would like to see lower contributing site values. Higher coverage may  lead to more contributing sites for noise.&#x20;