[ensembl-dev] VEP segmentation fault error

[Laurent Gil]

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 
> <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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