[ensembl-dev] VEP does not like whitespace in VCF input

[João Eiras]

On 14 May 2018 at 18:41, Andrew Parton <aparton at ebi.ac.uk> wrote:
> Hi João,
>
> Currently, VEP does not support blank lines within VCF files, however this is something that we intend to change in a future release. In the meantime however, you will need to remove blank lines from your input files for VEP to process them correctly.

Meanwhile I changed my pipeline to grep the input lines for non-whitespace.

But this was working find in version 87 when using the ensembl-tools
package, so I wonder if that was intended.

Also note that this only affects if there is whitespace before the
very first variant.

Thank you for the reply.