LoFreq / Blog: Recent posts

We've moved LoFreq's website and blog to http://csb5.github.io/lofreq/ !

There'll be no more updates on the website and blog here on sourceforge.

We will keep distributing source and binary packages through sourceforge though.

Andreas

Users rejoice: we've just released LoFreq 2.1!

The most important changes are the following:
- LoFreq can now call indels. Indel calling depends on a good alignment (use BWA-MEM and refine with lofreq viterbi), indel qualities (use lofreq indelqual or GATK's BQSR) and indel alignment qualities (computed internally). The feature is off by default, because it's still considered a bit suboptimal. To enable it, use --call-indels as extra argument for lofreq call and lofreq somatic.... read more

Jack OW has created a prototype Docker container for LoFreq which you can find here: https://registry.hub.docker.com/u/owjl/lofreq/

We are looking for people interested in testing the current alpha for LoFreq version 2.1. This version includes the ability to call (short) indels. Please send an email to me (wilma@gis.a-star.edu.sg) if you are interested, and indicate operating system (if you need binaries) and a brief explanation of what you're trying to do, so that we can give specific advice.

Once we get positive feedback, source-code and binaries will be released publicly here.... read more

We noticed performance issues with LoFreq 2.0.0 when running the somatic and call-parallel sub-command with bed-files containing many (i.e. thousands of) regions, which is for example the case in human exome analysis. This will be addressed in the upcoming release.

Andreas

PS: The next release will also come with source-code.

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).

We've finally released a beta version of the brand spanking new LoFreq-Star (AKA LoFreq 2.0)!

We'll soon update the webpage with more info, but installation (which just boils down to unpacking) and usage should be fairly straight-forward. This version includes a properly tested somatic SNV calling pipeline, which is already performing extremely well. We will add some more tweaks over the coming months to make it even better.... read more

This paper in Journal of Infectious Diseases used LoFreq to study population heterogeneity in bacterial (Mycobacterium tuberculosis) whole genome sequencing in a clinical setting.

We will release a beta-version of LoFreq* (AKA LoFreq2) in August. Amongst other enhancements, this version will include a thoroughly benchmarked somatic SNV calling pipeline.

We will soon release a beta of a rewritten and greatly extended version of LoFreq called LoFreq-Star. Amongst many other new features, LoFreq-Star is able to call low-frequency indels and features a highly sensitive and thoroughly benchmarked somatic SNV calling extension.

This is a minor release

• Anomalous reads (where a mate-pair is not mapped) can now taken into consideration with the new option -A, --anomalous-pairs-allowed (analogous to samtools mpileup -A)
• Overwriting of output files can be forced with the --force option

The frequencies listed in the snp-file for denv2-simulation.tgz were found to mixed up. The just uploaded package contains a corrected file and a corresponding vcf-file.

We've had reports about very strange results mostly on viral genomes. In such cases very few SNVs will be reported, with odd frequencies and very low coverage. We could trace this back to GATK's base call recalibration step, in which for yet unknown reasons, most base call qualities are set to the lowest possible value by GATK. We are investigating this and ask users to run LoFreq on the uncalibrated data in such cases (keeping in mind that spurious SNV calls are possible).

Changes:

• New option --cons-as-ref for cases where you want to call a consensus
  base per position and then call SNVs against it instead of calling SNVs against
  the given reference
• Default Bonferroni factor reverted to auto instead of auto-ign-zero-cov
• Removed Biopython dependency
• Added CONSVAR INFO field to vcf for denoting majority changes with regard to the reference base
• User supplied CFLAGS and LDFLAGS are passed down to Python's extension build as well

Changes:

• We are now also using read mapping qualities. This is achieved by joining base-call (P_bq) and mapping qualities (P_mq): P_joined = P_mq + (1-P_mq)*P_bq
• Now using GNU autotools for compilation and installation (./configure && make install)
• Now including a modified version of samtools mpileup
• Now including helper scripts to create a stringent, recalibrated mapping (bwa_unique.sh and base_qual_calib_wrapper.sh)
• Fixed mixup between --bonf options auto-ign-zero-cov and auto. The former is now default
• Added script lofreq_alnoffset.py which makes comparison of SNV calls made on different coordinate systems / against different reference sequences easier

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

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

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.

We've released version 0.2 last week, which now includes full run-time optimization and a number of small bug-fixes. The previous default to use LoFreq-NQ (quality agnostic EM-based modelling of substitution-type specific error-rates) as pre-filter to LoFreq-Q is now disabled, as LoFreq-Q is now fast enough even in ultra-high coverage regions (>>10k) and produces the same results with and without the filter.