[ensembl-dev] Duplicates in VEP for Plugins and Custom flags

[Kirsley CHENNEN]

Hi Will,
             There seems to be a bug in VEP (v81) for the use of Plugins 
and custom annotations. When theses parameters are specified in a config 
file, it seems that VEP imports them twice! This is even worse for 
custom annotations, as they are ouput twice and in a concatenated form! 
However, they behave normally, if the parameters are given in command 
line. Is it the only solution?


  Plugin example:
-------------------------
* In config file:
plugin               Blosum62


* Shell log:
[15-07-22 22:43:57] > ./variant_effect_predictor.pl --config 
cache/vep.ini -i example_GRCh37.vcf
...
version 81

By Will McLaren (wm2 at ebi.ac.uk)

Configuration options:

                    ##
allele_number      1
assembly           GRCh37
config             cache/vep.ini
core_type          core
dir xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache
dir_plugins 
xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache/Plugins
force_overwrite    1
fork               10
host               ensembldb.ensembl.org
input_file         example_GRCh37.vcf
minimal            1
offline            1
phased             1
plugin             Blosum62    Blosum62 <====
port               3306
species            homo_sapiens
stats              HASH(0x42c7728)
stats_text         1
terms              SO
variant_class      1
verbose            1

--------------------

2015-07-22 22:44:10 - Read existing cache info
2015-07-22 22:44:10 - Auto-detected FASTA file in cache directory
2015-07-22 22:44:10 - Checking/creating FASTA index
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <====
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <====
2015-07-22 22:44:10 - Starting...
2015-07-22 22:44:10 - Detected format of input file as vcf
2015-07-22 22:44:10 - Read 173 variants into buffer
2015-07-22 22:44:10 - Calculating consequences
[===============================================]  [ 100% ]
2015-07-22 22:44:11 - Writing output
2015-07-22 22:44:11 - Processed 173 total variants (173 vars/sec, 173 
vars/sec total)
2015-07-22 22:44:11 - Wrote stats summary to 
variant_effect_output.txt_summary.txt
2015-07-22 22:44:11 - Finished!



* In ouput file:
...
## BLOSUM62    : BLOSUM62 substitution score for the reference and 
alternative amino acids <====
## BLOSUM62    : BLOSUM62 substitution score for the reference and 
alternative amino acids <====
#Uploaded_variation    Location    Allele    Gene    Feature 
Feature_type    Consequence    cDNA_position
...






Custom example:
-------------------------
* In config file:
custom xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig


* Shell log:
[15-07-22 22:43:57]  > ./variant_effect_predictor.pl --config 
cache/vep.ini -i example_GRCh37.vcf
...
version 81

By Will McLaren (wm2 at ebi.ac.uk)
...
custom xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig 
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig
...

   * In ouput file:
...
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)

...


Best,
Kirsley



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