Certain sequencing artifacts can be distinguished by distinct noise profiles
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.
Note: Duplex bams are used for this calculation
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).