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

Will McLaren wm2 at ebi.ac.uk
Thu Feb 23 10:26:15 GMT 2012


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.


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
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