[GET-dev] Getting to the bottom of which variant one is looking at ?

Leon Peshkin peshkin at gmail.com
Tue Apr 10 16:13:38 EDT 2012

Hi everyone,
   after doing a whole bunch of curation at GET-e, I realized I am confused
at a very fundamental level - which
variant exactly is present in a given genome - I would appreciate some
feedback and help. Let's say there is
a variant
    Notch3   P34R  also known as rs1234
which corresponds to nucleotide C changing to G.
  the definition of rs...... often (but not always) has all possible
variants (C;C) (C;G) (G;G) like this one
rs4646    http://www.snpedia.com/index.php/Rs4646
  and your genome has allele frequency of 31%.
What exactly does it mean ? Where does zygosity annotation come from and
why is it missing in many variants?
Literature sometimes talks about rs1234 sometimes specifies nucleotide,
sometimes amino acid, plus sometimes there is confusion /inconsistency
among papers which strand the variant is on (if non-coding variants).

  Is there a way to facilitate the annotation by specifying the variant in
more than one way in GET-e ?

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