The changes in this PR regard would close issue #10 .
It implements the filter script within the VEP package as local module.
It accepts VEP-annotated input with multiple transcripts and adds two possibilities to filter for transcripts:
select a column and only filter for those transcripts, for which an entry (!=".") exists. This can be the PICK, CANONICAL or MANE_SELECT columsn annotated by VEP.
select transcripts based on simple list of transcripts to include.
It will remove all annotations of those variants without any matching transcript, but not remove the variant.
This needs to be considered for downstream processes.
The module enables the creation of MAF file formats with only one transcript, but can be adapted to individual needs.
The changes in this PR regard would close issue #10 .
It implements the filter script within the VEP package as local module. It accepts VEP-annotated input with multiple transcripts and adds two possibilities to filter for transcripts:
It will remove all annotations of those variants without any matching transcript, but not remove the variant. This needs to be considered for downstream processes. The module enables the creation of MAF file formats with only one transcript, but can be adapted to individual needs.