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Whats new in 4.67?

What's new in 4.67?

Posted: April 6 2023

This is a small release but adressing a recent problem affecting the clinical filter in particular of structural variants. Since VEP introduced a few new SO terms for functional annotation, and we introduced them to Scout and MIP this autumn, sometimes new causative variants have not been found with the clinical filter. Unfortunately the term splice_polypyrimidine_tract_variant has a slightly higher score than coding_sequence_variant - which is in clinical filter - in combination with filtering on most_severe_consequence rather than all transcript consequence can lead to missing variants that should have been found. Recognising that splice_polypyrimidine_tract_variant is most often insignificant for an SNV but more important in an SV, we have introduced an SV specific SO severity list, that contains this term, into the clinical filter.

Other features

Scout version 4.67 contains additional new features. This is the complete list of changes introduced from the previous one:

[4.67] CHANGELOG

Added

  • Prepare to filter local SV frequency

Changed

  • Clinical Filter for SVs includes splice_polypyrimidine_tract_variant as a severe consequence
  • Clinical Filter for SVs includes local variant frequency freeze ("old") for filtering, starting at 30 counts