[ensembl-dev] common string between input VCF and VEP output

[S Venkata Suresh Kumar]

Hi Will

Thanks.


On 02/23/2012 03:56 PM, Will McLaren wrote:
> Hello,
>
> If you supply a unique variant identifier in the third column of the
> VCF this will be used as the first column of the VEP output. If you
> don't have one, it is simple to create one and add it to your VCF
> using a simple perl script:
>
> perl -e '$i = 1; while(<>) { if(/^#/) { print; next;}  chomp; @a =
> split; $a[2] = "var".$i++; print join "\t", @a; print "\n";}'
> my_old.vcf > my_new.vcf
>
> In the next release of the VEP (due out in the next few days) you will
> be able to produce comprehensive output in VCF format using the --vcf
> flag, which will preserve the format of your input.
>
> Will
>
>
> On 23 February 2012 10:09, S Venkata Suresh Kumar
> <suresh.surampudi at india.semanticbits.com> wrote:
>> I was wondering if there is a common and unique string(s) between VCF
>> and VEP out put , to make one to one connection ? start and end
>> co-ordinates are good for substitutions, but not for insertions,
>> deletions and indels.
>>
>> regards
>> vs
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/