# Noise by Substitution Type

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**Theoretical Method**

For each position that crosses the noise threshold (usually set at 2%), base changes are counted for each of the 6 possible substitution types. 

{% hint style="info" %}
Note: Duplex bams are used for this calculation
{% endhint %}

**Technical Methods**

* Tool Used:
  * Marianas
  * Waltz PileupMetrics
  * calculate\_noise.sh
* Input
  * sample\_id-duplex-pileup.txt (for duplex noise calculation)
  * MSK-ACCESS-v1\_0-A-good-positions.txt (Pool A bed file with MSI regions removed)
* Output
  * noise-by-substitution.txt

**Interpretations**

ACCESS cfDNA samples usually exhibit larger noise values for C>T transitions, possibly due to cytosine deamination. However, differences between samples are not unexpected. Our threshold for ACCESS samples is 0.001 (past which we would fail a sample).