[ensembl-dev] VEP and ExAC plugin

Nicolas Thierry-Mieg Nicolas.Thierry-Mieg at imag.fr
Wed Aug 5 17:24:12 BST 2015


Hi all,

I'm experimenting with the ExAC plugin for VEP. I've noticed that I only 
obtain the global ExAC_AF but not the population-specific ExAC_*_AF 
values when using the --vcf option. Withouth this option it works.
Details follow.


For these tests I DL'd the latest VEP v81 available today, used 
INSTALL.pl, installed homo_sapiens_refseq_vep_81_GRCh37.tar.gz as a 
cache as well as the ExAC.pm plugin (both via INSTALL.pl). And I DL'd 
ExAC.r0.3.sites.vep.vcf.gz from the broad ftp.

$ more input.vcf
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	26131654	.	G	A	67.09	PASS		

$ variant_effect_predictor.pl -i input.vcf -o ttt.vcf --vcf --offline 
--refseq  --plugin 
ExAC,/home/nthierry/Software/ExAC/ExAC.r0.3.sites.vep.vcf.gz  --force
2015-08-05 17:34:41 - Read existing cache info
2015-08-05 17:34:41 - Loaded plugin: ExAC
2015-08-05 17:34:41 - Starting...
2015-08-05 17:34:41 - Detected format of input file as vcf
2015-08-05 17:34:41 - Read 1 variants into buffer
2015-08-05 17:34:41 - Reading transcript data from cache and/or database
[===============================================]  [ 100% ]
2015-08-05 17:34:41 - Retrieved 92 transcripts (0 mem, 236 cached, 0 DB, 
0 duplicates)
2015-08-05 17:34:41 - Analyzing chromosome 1
2015-08-05 17:34:41 - Analyzing variants
[===============================================]  [ 100% ]
2015-08-05 17:34:41 - Calculating consequences
2015-08-05 17:34:41 - Processed 1 total variants (1 vars/sec, 1 vars/sec 
total)
2015-08-05 17:34:41 - Wrote stats summary to ttt.vcf_summary.html
2015-08-05 17:34:41 - Finished!


So, it seems to run OK, but the produced ttt.vcf ends with |||||0.814||| 
. I would expect these (empty) fields to contain values.


If I remove --vcf from my command, the output vcf contains 
population-specific allele freqs, as expected, eg:
ExAC_AF_FIN=0.728;IMPACT=MODERATE;ExAC_AF=0.814;ExAC_AF_OTH=0.816;[...]

As a side note, as you can see without --vcf the fields are called 
ExAC_AF_* , but in the same file they are documented as ExAC_*_AF, eg:
## ExAC_EAS_AF	: ExAC East Asian Allele frequency
This last point is just a minor glitch, but you may want to fix it as well.


Regards,
Nicolas


-- 
-----------------------------------------------------------
Nicolas Thierry-Mieg
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
Pavillon Taillefer, Faculte de Medecine
38700 La Tronche, France
tel: (+33)456.520.067, fax: (+33)456.520.055
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