[ensembl-dev] VEP segmentation fault error

[Laurent Gil]

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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