Average Coverage, Sample Level, Pool A Targets

Detailed view of coverage values for each sample, grouped by UMI family type

Theoretical Method

Calculate average coverage of each of four possible bam types for each sample:

• Standard or “Uncollapsed”

• Collapsed unfiltered: after merging all reads from same UMI family

• Collapsed simplex: three or more reads found on one strand

• Collapsed duplex: one or more reads found on both strands (top and bottom)

Coverage is first averaged across each position in a single bait region. Then, the average across each bait region in the sample represents the sample’s final coverage value.

Technical Methods

• Tool Used:

  • Marianas

  • Waltz CountReads

  • aggregate_bam_metrics.sh

  • tables_module.py

  • plots_module.r

• Input

  • 4 bams per sample (Standard, U, S, D)

• Output

  • sample_id-intervals.txt (sample level, included for all 4 bam types)

  • waltz-coverage.txt (aggregated across samples, for a single bam type)

  • coverage_agg.txt (aggregated across all samples, all bam types, pools A / B)

Interpretations

Expected range of coverage values:

• • Raw coverage A panel:

    • ctDNA: ~ 15000x-20000x

    • Buffy Coat: ~ 500x-1000x

  • Raw coverage B panel:

    • ctDNA: ~ 1000x-1,500x

    • Buffy Coat: ~ 500x-1000x

  • Duplex coverage A panel:

    • ctDNA: ~ 500x-2000x

    • Buffy Coat: ~ 10x-50x