[ensembl-dev] VEP segmentation fault error

Tue Mar 6 09:09:12 GMT 2018

Dear Fazulur,

If you re-annotate a VCF file which has been already annotated by VEP, 
it will add all the annotations.

However you have 2 options when you run VEP on your already 
VEP-annotated VCF file:

1 - The default behaviour si to replace the "old" annotation (CSQ) by a 
"new" annotation
2 - You can keep the "old" annotation (CSQ) in the new VCF output and 
thus you will have 2 annotations per line, using the option "--keep_csq"

I hope it makes sense.

Best regards,

Laurent
Ensembl Variation

On 06/03/2018 07:10, Rehaman wrote:
> Dear Laurent,
>
> I have one more doubt regarding the vep annotations. I ran vep already 
> without gnomAD annotations before and I want to add the same now. Can 
> I run the same on annotated vcf file. Does it add again all the 
> annotations or only gnomAD frequencies. Since we already have 1000g 
> Allele frequencies, sift b scores etc in our annotated vcf. Does it 
> add again into new annotated vcf.
>
> Could you please suggest me.
>
> Thanks & Regards
> Fazulur Rehaman
>
> On Tue, Mar 6, 2018 at 7:28 AM, Rehaman <ensemblfan at gmail.com 
> <mailto:ensemblfan at gmail.com>> wrote:
>
>     Dear Laurent,
>
>     Thanks a lot for documentation page and explanation on custom
>     annotation feature.
>
>     As "--everything" option contains other annotations (--sift b,
>     --polyphen, --hgcs etc), can we use "--everything" and "--custom"
>     (for missing gnomAD allele frequencies) options together with vep.
>     Please confirm?
>
>     Thanks & Regards
>     Fazulur Rehaman
>
>     On Mon, Mar 5, 2018 at 5:38 PM, Laurent Gil <lgil at ebi.ac.uk
>     <mailto:lgil at ebi.ac.uk>> wrote:
>
>         Dear Fazulur,
>
>         You can see the explanations about the custom annotation
>         options (i.e. "exact" => "Annotation type"  and "0" => "Force
>         report coordinates" flag) in the VEP documentation page:
>
>         http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options
>         <http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options>
>
>         Best regards,
>
>         Laurent
>
>         On 05/03/2018 14:27, Rehaman wrote:
>>         Dear Laurent,
>>
>>         I have installed Bio:DB:HTS perl module and issue got
>>         resolved. Thanks a lot.
>>
>>         Could you please define what is "exact" and "0" custom
>>         annotation feature.
>>
>>         --custom
>>         gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,*vcf,exact,0,*AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH
>>
>>
>>         Thanks In Advance
>>         Fazulur Rehaman
>>
>>         On Thu, Mar 1, 2018 at 9:58 AM, Rehaman <ensemblfan at gmail.com
>>         <mailto:ensemblfan at gmail.com>> wrote:
>>
>>             Dear Laurent,
>>
>>             Thanks a lot for your response.
>>
>>             It was a typo. Actually I have used "--" before the
>>             custom option while running vep.
>>
>>             May be Segmentation fault error is due to Bio:DB:HTS perl
>>             module. I will run again after installing the same and
>>             let you know the status.
>>
>>             Please suggest me if error is not related to module.
>>
>>             Thanks & Regards
>>             Fazulur Rehaman
>>
>>
>>             On Wed, Feb 28, 2018 at 12:16 PM, Laurent Gil
>>             <lgil at ebi.ac.uk <mailto:lgil at ebi.ac.uk>> wrote:
>>
>>                 Dear Fazulur,
>>
>>                 Regarding your VEP command it looks like you missed
>>                 to add "--" before the "custom" option:
>>
>>                 *vep -i [vepdir]/examples/homo_sapiens_GRCh37.vcf
>>                 -cache --ASSEMBLY GRCh37 --fork 4 --custom
>>                 gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH*
>>
>>                 Best regards,
>>
>>                 Laurent
>>                 Ensembl Variation
>>
>>                 On 27/02/2018 19:04, Rehaman wrote:
>>>                 Dear Ensembl team,
>>>
>>>                 I am running VEP for GRCh37 assembly and as you
>>>                 mentioned some of alleles may not get Allele
>>>                 frequencies and so I want to test custom annotation
>>>                 optio
>>>
>>>                 I tried running vep with example vcf and getting
>>>                 "Segmentation Fault" error.
>>>
>>>                 Command:
>>>
>>>                 *vep -i [vepdir]/examples/homo_sapiens_GRCh37.vcf
>>>                 -cache --ASSEMBLY GRCh37 --fork 4 custom
>>>                 gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH*
>>>
>>>                 Could you please give me suggestions on this.
>>>
>>>                 Thanks & Regards
>>>                 Fazulur Rehaman
>>>
>>>
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>>
>>
>>
>
>
>

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