[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
>>>
>>>
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>>
>>
>>
>
>
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