[ensembl-dev] VEP segmentation fault error

[Rehaman]

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> 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> 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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