DuplexConsensusReads min-reads and max-reads-per-strand

[saty89]

Hi, I would like to clarify these parameters and some terminology as well as it's important for our clinical processing.

For DuplexConsensusReads, "Calls duplex consensus sequences from reads generated from the same double-stranded source molecule."_ it relies on GroupReadsByUMI (--paired) where it groups reads originating from the same source molecule and carry the same/similar (to include some error) UMI pairs.

Ideally, we expect atleast one UMI-pair for a double-stranded source molecule in the process.

1. To confirm that GroupReadsByUMI does not group different UMI-pairs even if the source molecule is the same (very rare) i.e. 5' and 3' positions same but UMI-pairs are different.

2. For min-reads, set to 2 1 1 -

   Do 2nd and 3rd values represent no. of reads required to create a single-strand consensus (SSC) sequence/read on each strand?

   Here 1 --> requires at least 1 raw read to create an SSC read on the top and bottom strand as both values are set to 1. If more reads are found supporting a single strand, it still collapses to 1 single-strand consensus read because max-reads-per-strand is always 1.

   For duplex (1st value), when set to 2, does it mean it requires 2 reads across both strands (and not 2 SSC reads), which in this case means one read from the top strand and one from the bottom strand to create a duplex consensus read?

   In general, creating a true duplex consensus read always results in only 1 SSC from each strand (varying no of reads supporting the SSC). And 2 SSC reads in total when the -- min-reads is set to 2 1 1.

   Is the understanding correct?

Appreciate your response. Thanks!