19 May 2015
A long overdue release with many, many smaller bug fixes and
improvements (almost would have justified a version bump to 2.2).
Main focus were the indel and somatic calling routines. By far the
biggest visible change is that we got rid of the consensus variants
(CONSVAR) concept and now assign qualities to all variants (in the
past CONSVARs could not be filtered based on quality)
See https://github.com/CSB5/lofreq/blob/master/Changelog for full details.
Andreas
17 Mar 2015
In Illumina data one can often observe low allele frequency indels in
poly-AT regions, which are likely false positives. GATK’s BQSR rarely
sets the corresponding indel qualities low enough though and so these
indels often get predicted by LoFreq and they are not automatically
removed. Newer versions of LoFreq (>=2.1.2) will indicate the length of
homopolymer runs in which an indel was predicted (see extra VCF field
called HRUN, akin to IonTorrent’s HRUN). Users might want to remove
indels associated with high values, especially when the predicted indel
ends in an A or T.
Andreas
06 Jan 2015
We have just created the
official Docker image for LoFreq
(currently version 2.1.1 and including samtools 1.1).
Andreas