Variant Annotation tools

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Contents

Working Group

Nicole Ruiz, Karen Eilbeck, Barry Moore, Shawn Rynearson

Documentation/Publications

Notes

The following tools will be used to annotate the exome of individual NA12878 from the 1000 Genomes project:

  • VAAST (the Variant Annotation, Analysis and Search Tool)
  • ANNOVAR
  • VAT (Variant Annotation Tool)
  • SeattleSeq
  • SNPeff
  • VEP (Variant Effect Predictor)
    • Current release: 73 (used release 71 for analysis)
    • Output default is text file but there is an option to output in VCF or GVF
    • Text file output column 7 is Consequence (variant effect)
    • SO terms are used to annotate
    • Prior to release 68, their own terms were used
    • Effects are not calculated for structural variants

Term Comparison

  • VAAST

VAAST.jpg

  • ANNOVAR

ANNOVAR.png

  • VAT

VAT.jpg

  • SeattleSeq

SeattleSeq.jpg

  • SnpEff

SnpEff.jpg

  • VEP

VEP.jpg

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