[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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