Dear All,


I am trying to run Shearwater and deep SNV to analyze exome-seq data.


In the deepSNV vignette

#==========

## Load data from deepSNV example

regions <- GRanges("B.FR.83.HXB2_LAI_IIIB_BRU_K034", IRanges(start = 3120, end
= 3140))

files <- c(system.file("extdata", "test.bam", package = "deepSNV"),
system.file("extdata",

"control.bam", package = "deepSNV"))

counts <- loadAllData(files, regions, q = 10)

dim(counts)

## [1] 2 21 10


## Run (bbb) computes the Bayes factor

bf <- bbb(counts, model = "OR", rho = 1e-04)


#==========

I have two questions:


1-How to create GRnages object for human reference genome, I have used
BSgenome package  as follows

 library(BSgenome.Hsapiens.UCSC.hg19) but i do not know how to proceed
further for obtaining reference genome as Granges object..


2-I  would like to know how can i specify rho value  in Bayes factor
calculation.

Any help is appreciated.

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