“On Bait” reads localized to ACCESS panel

Ensure there was adequate coverage of genomic regions in the ACCESS panel.

Theoretical Method

Divide the number of reads mapping to ACCESS genome bait regions by the sample’s total read count.

Note: This metric comes from the standard BAM

Technical Methods

• Tool Used:

  • waltz.jar CountReads

  • aggregate_bam_metrics.sh

  • tables_module.py

  • plots_module.r

• Input

  • ACCESS pool A and pool B bed files

  • Standard Bam (tables also produced for U / S / D bams)

• Output

  • Text file with the read count information: “sample_id.bam.read-counts.txt”

  • Text files for aggregated results “read-counts.txt”

Interpretations Ideally should be between 60%-80% and should not drop below 50% for ctDNA samples (A + B targets combined). Because A and B targets are mixed in 50:1 ratio, there should be a larger on-target rate for the A targets. If the rate drops below 50%, with adequate read counts, this could be indicative of a bad capture. For buffy coats, this is about 35%-45%.