[ensembl-dev] VEP segmentation fault error

[Rehaman]

Dear Laurent,

Thanks for your suggestions on annotated vcf and I will try the same and
let you know the status.

Thanks & Regards
Fazulur Rehaman

On Tue, Mar 6, 2018 at 12:09 PM, Laurent Gil <lgil at ebi.ac.uk> wrote:

> 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> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
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>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>
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