In 2011 we published HaploGrep, a way to assign haplogroups to mtDNA profiles. It is now the defacto standard for haplogroup assignment with currently >2k users each month.
Over the last years we (especially Hansi) improved the software and I’m happy to announce that it has been accepted by the NAR Web Server Issue 2016.
Main Features of HaploGrep2
- Rule-based system allows to detect artificial recombinants and missing variants as well as annotating rare and phantom mutations
- Import VCF files
- Generate a publication ready graphical tree
- New export formats (VCF, multiple sequence alignment format, extended reports)
- New metrics (Hamming distance, Jaccard index, Kimura 2-parameter)
- Haplogroup discordance calculation between all 4 metrics
- Providing a Restlet API and a command line version of HaploGrep