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splice_region_variant has lower priority than synonymous_variant #44
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Sequence ontology terms On the other hand, For v1.7, a major change is to remove the custom EffectPriority and BiotypePriority, and instead rely on VEP to do the ranking. As of VEP v79, vcf2maf uses the arguments |
Sounds good. Thanks! |
Released v1.6.7 with a fix. MAFs from this release will contain a This does not comply with MAF spec v2.4. But per a chat with a TCGA lead, we can unofficially make as many changes as we like, that don't break too many existing MAF parsers. If we want to make it official, we have to wait for the responsibility to transfer from NCI's TCGA to NCI's GDC, before we propose changes to the MAF specs. Regd v1.7 mentioned earlier in this thread, it's backlogged because the VEP way of prioritizing effects needs more testing before we use it across MSKCC. |
17:g7579312C>A is annotated as silent mutation, but according to VEP the most severe consequence is splice_region_variant.
http://grch37.rest.ensembl.org/vep/human/hgvs/17:g7579312C%3EA?content-type=application/json
I think we should assign a lower priority to synonymous_variant.
Alternatively, is it possible to assign the most_severe_consequence from VEP as the annotated consequence in MAF?
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