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Hi Will,<br>
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?<br>
<br>
<br>
Plugin example:<br>
-------------------------<br>
* In config file:<br>
plugin Blosum62<br>
<br>
<br>
* Shell log:<br>
[15-07-22 22:43:57] > ./variant_effect_predictor.pl --config
cache/vep.ini -i example_GRCh37.vcf<br>
...<br>
version 81<br>
<br>
By Will McLaren (<a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
##<br>
allele_number 1<br>
assembly GRCh37<br>
config cache/vep.ini<br>
core_type core<br>
dir
xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache<br>
dir_plugins
xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache/Plugins<br>
force_overwrite 1<br>
fork 10<br>
host ensembldb.ensembl.org<br>
input_file example_GRCh37.vcf<br>
minimal 1<br>
offline 1<br>
phased 1<br>
plugin Blosum62 Blosum62 <font
color="#ff0000"><====</font> <br>
port 3306<br>
species homo_sapiens<br>
stats HASH(0x42c7728)<br>
stats_text 1<br>
terms SO<br>
variant_class 1<br>
verbose 1<br>
<br>
--------------------<br>
<br>
2015-07-22 22:44:10 - Read existing cache info<br>
2015-07-22 22:44:10 - Auto-detected FASTA file in cache directory<br>
2015-07-22 22:44:10 - Checking/creating FASTA index<br>
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <font
color="#ff0000"><====</font><br>
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <font
color="#ff0000"><====</font><br>
2015-07-22 22:44:10 - Starting...<br>
2015-07-22 22:44:10 - Detected format of input file as vcf<br>
2015-07-22 22:44:10 - Read 173 variants into buffer<br>
2015-07-22 22:44:10 - Calculating consequences<br>
[===============================================] [ 100% ]<br>
2015-07-22 22:44:11 - Writing output<br>
2015-07-22 22:44:11 - Processed 173 total variants (173 vars/sec,
173 vars/sec total)<br>
2015-07-22 22:44:11 - Wrote stats summary to
variant_effect_output.txt_summary.txt<br>
2015-07-22 22:44:11 - Finished!<br>
<br>
<br>
<br>
* In ouput file:<br>
...<br>
## BLOSUM62 : BLOSUM62 substitution score for the reference and
alternative amino acids <font color="#ff0000"><====</font><br>
## BLOSUM62 : BLOSUM62 substitution score for the reference and
alternative amino acids <font color="#ff0000"><====</font><br>
#Uploaded_variation Location Allele Gene Feature
Feature_type Consequence cDNA_position <br>
...<br>
<br>
<br>
<br>
<br>
<br>
<br>
Custom example:<br>
-------------------------<br>
* In config file:<br>
custom
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig<br>
<br>
<br>
* Shell log:<br>
[15-07-22 22:43:57] > ./variant_effect_predictor.pl --config
cache/vep.ini -i example_GRCh37.vcf<br>
...<br>
version 81<br>
<br>
By Will McLaren (<a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
...<br>
custom
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig<br>
...<br>
<br>
* In ouput file:<br>
...<br>
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)<br>
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)<br>
<br>
...<br>
<br>
<br>
Best,<br>
Kirsley<br>
<br>
<br>
<br>
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