[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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