Release of 2.1.1 (bug fix release)

A last minute bug sneaked into version 2.1.0 (just released yesterday). It was triggered when calling SNVs and indels simultaneously with lofreq call (not somatic) and would have resulted in a segfault in most cases (at the automatically run filtering stage).

The actual reason was broken indexing during the FDR correction for strand-bias filtering when indels and SNVs where present in the same vcf file. The somatic pipeline was not affected by this because it keeps separate files for SNVs and indels.

Andreas

Move to github

We have permanently moved LoFreq’s website and blog to a new home on github

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

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

Andreas

Release of LoFreq 2.1

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.
• Parameters for somatic calls are now thoroughly tested
• Release of MIT licensed source code
• LoFreq is now compiled against an external version of samtools and htslib (1.1)
• bgzip and tabix support (all output from somatic is now bgzipped)
• Run-time issue with bed-files containing thousands of regions (e.g. human exome) has been resolved
• Lots of other tiny bug-fixes and improvements

This release comes as a binary package for Linux and MacOSX and now also with MIT-licensed source-code. Please have a look at the files section on sourceforge.

Usage has changed slightly, but should be obvious from the commandline help of LoFreq’s subcommands. We will be updating the online documentation soon after we’ve moved source code and website to github and github-pages (will be announced here) so check back soon!

Andreas