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Additional annotation from ExAC and 1000G
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@supernifty supernifty released this 14 Dec 00:47
v2.4.1
83cc2bc

Due to issues with VEP's annotation of ExAC and 1000G datasets, Cpipe now adds these annotations separately, using a normalised version of the ExAC (0.3.1) and 1000G (phase 3) VCFs.

  • These VCFs have been added to the set of Cpipe assets (in data/annotation)
  • vcfanno has been added as a stage to the pipeline.
  • The vcfanno stage by default adds annotation for ExAC and 1000G, but can be customised by modifying pipeline/vcfanno.config.
  • Redundant fields from VEP and dbNSFP have been removed.
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