Translate HGVS annotation from one transcript to the MANE-select transcript using VEP

Question

[genomics2023]

Hi all,

I've been having an issue in using VEP to translate an HGVS annotation from one transcript to the MANE-select transcript.

Using --mane or --mane_select it adds a flag indicating if the transcript is the MANE Select or MANE Plus Clinical transcript but I'm interested in receiving as output only the protein change annotated on the MANE Select transcript.

Would you be able to help me?

Thank you so much!

[Ram]

MANE/MANE Select is an annotation and I've found that retaining more annotations and filtering them downstream is a more sustainable/long-term solution than asking the annotator to remove records at output time.

I personally use bcftools +split-vep | awk to filter VEP output. Along with the ability to select only records where MANE=1/YES/whatever_the_positive_indicator_is, you can use options such as -s worst to pick the worst consequence per variant, which is often on the MANE transcript. There's also the vep_filter tool from EnsEMBL.