is there any option how to choose my own list of transcripts when I using VEP for annotation. I would like to have some option something like SnpEff has:
SnpEff allows you to provide a list of transcripts to use for annotations by using the -onlyTr file.txt and providing a file with one transcript ID per line. Any other transcript will be ignored.
$ java -Xmx4G -jar snpEff.jar -onlyTr my_transcripts.txt GRCh37.75 test.chr22.vcf > test.chr22.ann.vcf
As far as I know in VEP is possible just use option for canonical OR all transcripts. I would like to avoid to parsing VCF with all type of transcript.
Thank you for any idea.