[ensembl-dev] VEP variants missing on output

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Wed May 22 09:09:25 BST 2013


It doesn't. I just dropped it because Will said it could be buggy.


On 05/22/2013 10:07 AM, Duarte Molha wrote:
>
> So using the html misses variants?
>
> *From:*dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On 
> Behalf Of *Guillermo Marco Puche
> *Sent:* 22 May 2013 08:23
> *To:* dev at ensembl.org
> *Subject:* Re: [ensembl-dev] VEP variants missing on output
>
> Hello Will,
>
> You was right. I'm getting the 406 variants.
> I just dropped html in case.
>
> As always flawless Ensembl support. Thank you !
>
> Best regards,
> Guillermo.
>
> On 05/21/2013 05:13 PM, Will McLaren wrote:
>
>     You get one line of output for each variant/feature overlap, so
>     you will almost always see more output lines than input if you use
>     the default output format. If you use VCF output, you only get one
>     line per variant.
>
>     You can check how many unique variants there are in the output
>     with e.g.:
>
>     grep -v # variant_effect_output.txt | cut -f 1 | sort -u | wc -l
>
>     assuming your variants have unique names.
>
>     Try dropping "html" from your config, see if that makes any
>     difference - as the newest feature there, it's got a higher chance
>     of causing problems!
>
>     Will
>
>     On 21 May 2013 16:02, Guillermo Marco Puche
>     <guillermo.marco at sistemasgenomicos.com
>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     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  <http://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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