Variant annotation in Python
Project description
Varcode is a Python library for predicting the impact of genomic variants on protein sequences.
Effect Types
Intergenic
Intragenic
IncompleteTranscript
NoncodingTranscript
Intronic
ThreePrimeUTR
FivePrimeUTR
Silent
Substitution
Insertion
Deletion
ComplexSubstitution
AlternateStartCodon
IntronicSpliceSite
ExonicSpliceSite
StopLoss
SpliceDonor
SpliceAcceptor
PrematureStop
FrameShiftTruncation
StartLoss
FrameShift
ExonLoss
Coordinate System
Varcode currently uses a “base counted, one start” genomic coordinate system, to match the Ensembl annotation database. We are planning to switch over to “space counted, zero start” (interbase) coordinates, since that system allows for more uniform logic (no special cases for insertions). To learn more about genomic coordinate systems, read this [blog post](http://alternateallele.blogspot.com/2012/03/genome-coordinate-conventions.html).
Project details
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