Contributing Sites for Noise

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

Theoretical Method

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

Note: Duplex bams are used for this calculation, and only substitutions are included, not insertions or deletions

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.