# Average Coverage, Sample Level, Pool A Targets

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**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