[ensembl-dev] VEP segmentation fault error

Rehaman ensemblfan at gmail.com
Thu Mar 1 04:28:59 GMT 2018


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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