[ensembl-dev] Effects predictor version 2

[Stuart Meacham]

Hi,

I am trying to use the updated version of the Effects predictor (version 
2). I have it running now but I came across a couple of issues:

I found it impossible to pass DB parameters to the script to define, for 
example, a local version of the latest human core DB. Looking at the 
code it seems that the script is expecting a 'host' parameter yet the 
README states a 'db_host' parameter (the 'd' option does not work 
either). Despite noticing this I still couldn't get it to work via 
command line options. In fact I had a lot of trouble passing any 
short-form options, instead I had to define a registry file, which 
worked fine.

On running I get a warning about version numbers however I have only 
just downloaded and installed the latest API libs and created the core 
DB today. The warning is strange anyhow in that it states my DB version 
is 62 and my software version is 63 (which I didn't think had been 
released yet!).

The script silently over-writes an existing output file of the same 
name, this seems a bit brutal, perhaps the default should be to fail if 
the file exists.

I don't seem to get any Polyphen or Sift predictions. My command is:

perl ./variant_effect_predictor_2.pl -r reg.pl -i ./variants.txt.vcf 
--format vcf -w -b 100000 --sift=p --polyphen=p --failed=0 -terms=so

and after analysing chr 1 with 360,000 variants I don't see any 
predictions. Maybe this is to be expected, I'm a bit clueless about this 
I'm afraid.

Cheers

Stuart