Distribution of ACCESS panel A coverage values

Ensure consistent coverage across ACCESS bait (or “probe”) regions

Theoretical Method

Coverage of each genomic region in the ACCESS panel is grouped on a per-sample basis, and a distribution of these values is plotted. Each sample is normalized by the median coverage value of that sample to align all peaks with one another and correct for sample-level differences.

Technical Methods

• Tool Used:

  • Waltz CountReads

  • aggregate_bam_metrics.sh

  • tables_module.py

  • plots_module.r

• Input

  • Collapsed, unfiltered bam

  • ACCESS pool A bed file

• Output

  • intervals-coverage-sum.txt (one per bam type / pool combination)

  • coverage_per_interval.txt (one per sample / bam type / pool combination)

  • coverage_per_interval_A_targets_All_Unique.txt (this is used for graph above)

    • (DMP specific format?)

Interpretations Each distribution should be unimodal, apart from a second peak on the low end due to X chromosome mapping from male samples. Narrow peaks are indicative of evenly distributed coverage across all bait regions. Wider distributions indicate uneven read distribution, and may be correlated with a large GC bias. Note that the provided bed file lists start and stop coordinates of ACCESS design probes, not the actual genomic target regions.