About

We (Hansi, Sebastian and Lukas) are three computer scientists working at the Division of Genetic Epidemiology, Medical University Innsbruck. We are especially interested in presenting scalable and usable services to the community.
In this blog, we talk about mtDNA in general, HaploGrep and our Hadoop MapReduce experiences.

People

Hansi Weissensteiner Contact
Sebastian Schönherr Contact
Lukas Forer Contact

We have a strong cooperation with the research group of Databases and Information Systems (DBIS), University of Innsbruck.
We also want to say thanks to all the fruitful discussions, especially with our collaborators Antonio Salas and Hans Bandelt.

2 thoughts on “About

  1. Mick Reed says:

    Hi

    I’ve seen a couple of sequences recently that have been put through Haplogrep as follows:

    One had 313.1C and the other had 314.1C whereas usually these show as 315.1C, since they are ‘errors of nomenclature’ and should normally be expressed as 315.1C.

    In each case, Haplogrep shows a ‘global private mutation’ whereas other software normally corrects for this ‘error of nomenclature’

    Any comments? Or am I misunderstanding something?

    Cheers

    Mick

  2. Hansi says:

    Hi Mick!

    Did you upload FASTA files or are the variants generated with another tool? Since I’m working on the FASTA Import for HaploGrep2, this is in a beta state and will be tweaked. So far we didn’t correct variant files uploaded from users – we can however add an additional hint with the new rule-based quality check. We still want the users to recheck their results.

    Position 315.1C is a so called hotspot, besides 309.1C(C), AC indels at 515-522, 16182C, 16183C, 16193.1C(C) and 16519. Those were not considered for phylogenetic reconstruction and are excluded from Phylotree and are not relevant for a haplogroup classification.

    Global Private Mutation means that a variant is not known by Phylotree, therefore getting a weight of 0 and is not considered in the process of haplogroup classification. So in your case it doesn’t influence the classification. Hope this helps,

    best,
    Hansi

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