phiX


Data from two phiX experiments sequenced on a GAIIx.


This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.

Moritz Gerstung

deepSNV

Detection of subclonal SNVs in deep sequencing data.

phiX function

Data from two phiX experiments sequenced on a GAIIx.

phiX: Example phiX data

Description

Arguments

Examples