We’ve just released version 2.0.0, which includes an updated core logic to handle all sources of errors separately, new default, high specificity settings for the somatic SNV caller, support for parallel calls even on single chromosome/sequence mappings and many tiny improvements and bug fixes. Note, we had to change the arguments names of the ‘call’ subcommand. The usage document has been updated to reflect this.
The Second Beta contained a couple of debug messages the were unnecessary and annoying and also slowed things down. Furthermore this new beta allows to use orphaned reads from read-pairs.
We’ve just released the second beta version of LoFreq-Star (AKA LoFreq 2.0)! This second beta has kept us busy for a while and a corresponding webpage is still missing, but we’re working on it. As before, just unpack the tarball and you can directly use the binary in ./ lofreq/lofreq (please do not change the directory layout or link to that binary).