[ensembl-dev] VEP segmentation fault error

Laurent Gil lgil at ebi.ac.uk
Tue Mar 6 09:14:26 GMT 2018


Dear Fazulur,

I don't see any problem to use the "--everything" and "--custom" options 
together.

Best regards,

Laurent
Ensembl Variation

On 06/03/2018 04:28, Rehaman 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
>>>
>>>
>>>             _______________________________________________
>>>             Dev mailing listDev at ensembl.org <mailto:Dev at ensembl.org>
>>>             Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>             <http://lists.ensembl.org/mailman/listinfo/dev>
>>>             Ensembl Blog:http://www.ensembl.info/
>>
>>
>>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20180306/f427110d/attachment.html>


More information about the Dev mailing list