[ensembl-dev] Variant effect predictor

Henrikki Almusa henrikki.almusa at helsinki.fi
Wed Jun 15 13:05:49 BST 2011


I'm testing the variant effect predictor (2.0 against local copy of 
ensembl 62) and noticed some things.

1. When I run one sample' indels with it, the resulting list has lines 
which start with '+' instead of the uploaded variation information. What 
causes this?

2. It seems that the whole_genome option switches off the gene name. Is 
there an option to switch it back on? I could use HGNC to get that name, 
but would still lack the ensembl identifier.

3. The variant effect predictor seems to be able to read in the ucsc 
used 'chr1' type chromosomes. However it does stumble with 'chrM' which 
is 'MT' in ensembl.

Henrikki Almusa

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