UMI Family types Composition (Pool B)

Understanding the relative abundance of each fragment subtype (for Pool B probe regions)

Theoretical Method

Similarly to the Pool A metrics, the UMI family type composition is here presented for Pool B targets. Buffy coat samples should have comparable UMI family composition for both Pools A and B.

Technical Methods

• Tool Used:

  • Marianas

  • make_umi_qc_tables.sh

  • plots_module.r

• Input

  • Marianas collapsed fastqs

• Output

  • family-types-B.txt

Interpretations

Duplex families are valuable for their low noise rate after collapsing, thus we'd like to see as high of a duplex "saturation" as possible. Because Pool B probes are mixed at a lower ratio in the capture process for cfDNA samples, they will have less duplex saturation. If this value is lower, we may not have captured enough of the original molecules to find both strands after PCR replication.