New
3.0.0
What's Changed
The major change in 3.0 comes in an update to our UMI-based consensus callers, and the inclusion of a new consensus caller for CODEC sequencing data (CallCodecConsensusReads). In addition to the new caller, the following updates were made:
GroupReadsByUminow correctly segregates read pairs with the same coordinates and UMIs but where R1 and R2 are swapped- All consensus callers now support a
--rejectsoption to write reads not used in consensus calling to a BAM file- Reads in the BAM files are also tagged with the reason they were rejected in the
rrtag
- Reads in the BAM files are also tagged with the reason they were rejected in the
- All consensus callers now support a
--statsoption which will output a text file with a table of statistics generated during consensus calling FilterConsensusReadsprevious--max-no-call-fractionoption has been changed to and is now interpreted as a fraction if less than 1.0, or as a count of no-call bases if greater than or equal to 1.0.