[ensembl-dev] VEP and ExAC plugin
Nicolas Thierry-Mieg
Nicolas.Thierry-Mieg at imag.fr
Thu Aug 6 10:46:19 BST 2015
Hello,
confirmed fixed, thanks Will!
Regards,
Nicolas
On 08/06/2015 11:33 AM, Will McLaren wrote:
> Hi Nicolas,
>
> Thanks for the report - some of the headers were getting scrambled
> internally.
>
> I've pushed fixes to release/81 of ensembl-tools (the
> variant_effect_predictor.pl <http://variant_effect_predictor.pl> script)
> and the ExAC.pm plugin file - please re-download VEP and re-run the
> installer.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 5 August 2015 at 17:24, Nicolas Thierry-Mieg
> <Nicolas.Thierry-Mieg at imag.fr <mailto:Nicolas.Thierry-Mieg at imag.fr>> wrote:
>
> 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 <http://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
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