Noise by Substitution Type

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).