Raw read-pair counts (standard BAM)

Validating the correct number of reads obtained from the sequencer

Theoretical Method

Total number of reads sequenced. Obtained from iterating through SAMRecord instances in Standard Bam file.

Technical Methods

• Tool Used

  • Waltz.jar CountReads

  • tables_module.py

  • plots_module.r

• Input

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

• Output

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

Interpretations

ACCESS is designed to target ~50-80M reads per ctDNA sample, and ~5-10M reads for buffy coat samples. This number should be independent of the amount of library input DNA as well as coverage values, as PCR will bring low input values up to a consistent amount for sequencing.