HaploGrep2 Update 2.1.21

With HaploGrep version 2.1.21 the handling of human mitochondrial FASTA sequences gets a new improvement. As we use BWA 07.17 for the alignment of FASTA sequences, the mtDNA nomenclature is not always met by default. Therefore we provide a new parameter which will fix the nomenclature to the correct one used in Phylotree, finally yielding a better HaploGrep score. The parameter is:

--fixNomenclature

Currently we apply 66 rules, which will fix issues around indels (insertions and deletions) – e.g.  the deletion on 8281-8289d for haplogroup B, but also around 315 and 524 (which are however not relevant for the mitochondrial phylogeny)