[ensembl-dev] VEP variants missing on output
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue May 21 16:02:57 BST 2013
Hello Will,
I'm getting more 3000 lines of file output.. this seems really weird....
wc -l variant_effect_output.txt
*3936*
Here's the way I'm proceeding:
./variant_effect_predictor.pl -i /home/likewise-open/SGNET/gmarco/vep_71_annotation_check/input.vcf -force -fork 4 --database --config vep_71.test
Here's the content of vep_71.test:
dir /home/likewise-open/SGNET/gmarco/.vep
toplevel_dir /home/likewise-open/SGNET/gmarco/.vep
force_overwrite 1
format vcf
html 1
host 192.19.x.xx
port 3306
user myuser
password mypassword
buffer_size 5000
hgvs 1
canonical 1
ccds 1
check_svs 1
domains 1
gmaf 1
hgnc 1
maf_1kg 1
numbers 1
polyphen b
regulatory 1
sift b
Best regards,
Guillermo.
On 05/21/2013 02:30 PM, Will McLaren wrote:
> Hi Guillermo,
>
> I'm unable to recreate this, sorry!
>
> I get 406 going in, 406 coming out every time, whichever combination
> of those options above I use, and whether I use VCF or standard output.
>
> Here's my run (minus -check_sv):
>
> > perl variant_effect_predictor.pl
> <http://variant_effect_predictor.pl> -i guill.vcf -vcf -cache -force
> -fork 4 -hgvs -canon -ccds -domains -gmaf -hgnc -maf_1kg -numbers
> -poly b -regu -sift b -fasta
> ~/NFS/Fasta/Homo_sapiens.GRCh37.69.dna.primary_assembly.fa
> 2013-05-21 13:24:26 - Checking/creating FASTA index
> 2013-05-21 13:24:26 - Read existing cache info
> 2013-05-21 13:24:26 - Starting...
> 2013-05-21 13:24:26 - Detected format of input file as vcf
> 2013-05-21 13:24:26 - Read 406 variants into buffer
> 2013-05-21 13:24:26 - Reading transcript data from cache and/or database
> [================================================================] [
> 100% ]
> 2013-05-21 13:24:30 - Retrieved 10891 transcripts (0 mem, 10919
> cached, 0 DB, 28 duplicates)
> 2013-05-21 13:24:30 - Reading regulatory data from cache and/or database
> [================================================================] [
> 100% ]
> 2013-05-21 13:24:35 - Retrieved 36955 regulatory features (0 mem,
> 36955 cached, 0 DB, 0 duplicates)
> 2013-05-21 13:24:35 - Calculating consequences
> [================================================================] [
> 100% ]
> 2013-05-21 13:24:56 - Writing output2013-05-21 13:24:56 - Processed
> 406 total variants (14 vars/sec, 14 vars/sec total)
> 2013-05-21 13:24:56 - Wrote stats summary to
> variant_effect_output.txt_summary.html
> 2013-05-21 13:24:56 - Finished!
> > wc -l variant_effect_output.txt
> 408
>
> It's 408 as it's adding two header lines to the VCF output.
>
> Which 16 are missing from your output, and is it the same 16 each time?
>
> Try writing to a different output file, or on a different disk if you
> can (perhaps disk space is an issue?)
>
> Will
>
>
> On 21 May 2013 13:15, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> Hello Will,
>
> Here's the input:
> https://github.com/guillermomarco/vep_plugins_71/blob/master/missing_variants/missing_output_variants.vcf
>
> As you said it's not about the options or plugins. Launching VEP
> without specyfiying any option still returns an output with
> missing variants.
>
> Regards,
> Guillermo.
>
>
>
> On 05/21/2013 01:49 PM, Will McLaren wrote:
>> Hi Guillermo,
>>
>> None of those options should filter out variants.
>>
>> Are you able to provide any of the files that recreate the problem?
>>
>> Is there any chance that you are using VCF input and it contains
>> non-variant lines - this would be where the ALT column is empty
>> or "."? If so, this may be your problem. To force these to be
>> included in the output, you should add --allow_non_variant.
>>
>> Regards
>>
>> Will
>>
>>
>> On 21 May 2013 09:40, Guillermo Marco Puche
>> <guillermo.marco at sistemasgenomicos.com
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>> Hello,
>>
>> I've been checking VEP results, and i've noticed that I'm
>> missing some input variants in the output.
>>
>> I think this may be issued to some of the options i'm using
>> to launch vep:
>>
>> hgvs 1
>> canonical 1
>> ccds 1
>> check_svs 1
>> domains 1
>> gmaf 1
>> hgnc 1
>> maf_1kg 1
>> numbers 1
>> polyphen b
>> regulatory 1
>> sift b
>>
>> Should be any of these options filtering output? I've
>> disabled all plugins to run this test to be sure that it's
>> not a plugin issue.
>>
>> * With a 406 variant input vcf file, I've missed 16 variants.
>> * I then ran VEP with only those 16 missing variants and
>> missed 3 on output.
>> * Rerun again and now with 3 missing variants and now not a
>> single one was missing.
>>
>> I would like to know what's behind that weird behaviour.
>>
>> Thank you.
>>
>> Best regards,
>> Guillermo.
>>
>>
>>
>>
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