Average Coverage, Sample Level, Pool B Targets

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

Theoretical Method

Similarly to the Pool A Targets, coverage is calculated for each UMI family type, over the Pool B genomic bait regions. These coverage values are lower for cfDNA samples (which use a 50:1 pool ratio) but should be comparable for buffy coat samples (which use a 1:1 pool ratio).

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 Aim is to have high coverage, and as much duplex “saturation” as possible. See title page for specific pass / fail criteria.