min-base-quality recommendation

[gevro]

Hi, There is no default value for min-base-quality in FilterConsensusReads, and I'm a bit unclear on the exact format of setting this, and also how consensus base qualities are encoded by CallMolecularConsensusReads.

1. Is there an upper limit on phred scores output by CallMolecularConsensusReads? I'm assuming these Phred scores per base of the consensus are encoded in the standard base quality column of the bam file? Since duplex sequencing can go as low as 10-7, standard quality encoding ranges will not work.

2. I'm assuming for 'min-base-quality' in FilterConsensusReads that setting this to a value of 10 = an error rate of 0.1?

3. The documentation of FilterConsensusReads says that min-base-quality has a max value of 1. Is 1 the setting for no filter? If so, isn't 1 technically the minimum rather than maximum value? Because if I would want to increase the threshold, I would need to set it as a phredscore cutoff of 10, 20, etc, which are larger values than 1.

Thanks.

[nh13]

https://github.com/fulcrumgenomics/fgbio/issues/662#issuecomment-786482347

[gevro]

Note also issue #666. I posted it without the full question by mistake before the comment was closed. I'm linking here in case you don't get notifications on closed comments.