[ensembl-dev] VEP segmentation fault error

[Rehaman]

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> 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
>
> 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> 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> 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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