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