LoFreq as Docker container

Jack OW has created a prototype Docker container for LoFreq

Alpha testers for release 2.1 needed

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 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.

Andreas

PS: We assume you already have BAM files (created with BWA or BWA-MEM), duplicates were removed, indels were realigned and base-qualities recalibrated (with GATK>=2).

Performance issues when using bed-file with many regions

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.