The split-vep plugin is very useful and I would like to use it to split the ANN field created by SnpEff. This should be theoretically possible but it seems that the plugin is hardcoded to require that there is a field named Consequence.
The INFO description also requires that the format be designated by Format: <field>|<field2>|<field3>
I am wondering if it might be possible to make split-vep a little more flexible by allowing a manual override of these on the CLI.
Something like --fields with --consequence-field (if a consequence field is in fact required at all)?
This is preferable to editing the header to me because it would require fewer operations on the file.
The
split-vepplugin is very useful and I would like to use it to split theANNfield created bySnpEff. This should be theoretically possible but it seems that the plugin is hardcoded to require that there is a field namedConsequence.The
INFOdescription also requires that the format be designated byFormat: <field>|<field2>|<field3>I am wondering if it might be possible to make
split-vepa little more flexible by allowing a manual override of these on the CLI.Something like
--fieldswith--consequence-field(if a consequence field is in fact required at all)?This is preferable to editing the header to me because it would require fewer operations on the file.