About

In this blog, we (@seppinho, @lukfor and @whansi) are talking about mtDNA, HaploGrep and mtDNA-Server.

 

 

3 thoughts on “About

  1. 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. 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

    1. Hi Hansi,

      Are you, by chance, working on the FASTA import right now? It’s a great feature, we love it and have used it successfully before, but today I am either getting errors about having only 2 import fields or just get stuck uploading sample data (~115 genomes) for hours on end.

      Cheers,
      Ana

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