How to select predefine transcript when annotate VCF

Question

[Paul]

Dear all,

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.

Answer 1

[Paul]

I found solution in module - filter_vep.pl - there you can filter out just transcript, which you need. Syntax is: --filter "Feature is YOUR_TRANSCRIPT_ID"