Version 0.4.0 released

Changes:

• Fixed overflow for very large Bonferroni factors (affected auto- Bonferroni option on WGS of HG, for example)
• Reported base-counts and frequencies are now unfiltered, with the exception of Q<3 which is always removed
• Added Bonferroni option ‘auto-ign-zero-cov’
• Added –force option for forced overwriting of files

Version 0.3.2 released

Changes:

• The Bonferroni factor for SNV quality filtering is now by default determined and applied automatically in lofreq_snpcaller.py
• LoFreq now checks for a working samtools installation during setup
• lofreq_uniq_pipeline.py now summarizes the result files

Version 0.3.1 released

We’ve just released version 0.3.1. The most visible changes are (i) LoFreq’s output is now chromosome aware (an overdue feature), (ii) the Samtools pileup is now generated internally (no more messing with samtools by the user needed), (iii) the added support for region bed files (which allows to restrict the analysis to regions) and (iv) the addition of the LoFreq unique pipeline script (for e.g. easy somatic snv calls) and a couple more helper scripts.