[ensembl-dev] VEP segmentation fault error

[Rehaman]

 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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