Validating the correct number of reads obtained from the sequencer
Total number of reads sequenced. Obtained from iterating through SAMRecord instances in Standard Bam file.
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”
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.