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Cancer Bayesian Selection Estimation (CBaSE)

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Usage

Running CBaSE

python 

Input file format

Gene symbolMutation effect Mutated nucleotide Context index
ECE1 coding-synon C 38
SAMD11 missense A 29
TNFRSF4 nonsense A 28

(1) Gene symbol

  Corresponds to the official gene symbol as used in the UCSC knownGene track.

(2) Mutation effect

  One of ["missense", "nonsense", "coding-synon", "intron", "utr-3", "utr-5", "IGR"] ("intron" and "IGR" mutations are discarded).

(3) Mutated nucleotide

  One of [A, C, G, T].

(4) Context index

  0-based indices of trinucleotide contexts can be looked up here.

CBaSE tool

You can also find a web-based user interface for CBaSE here: http://genetics.bwh.harvard.edu/cbase/index.html