[BioC] Create consensus fasta file from indexed Bam file

Jacques LE GOUIS [guest] guest at bioconductor.org
Wed Jun 19 11:54:32 CEST 2013

I have an indexed bam files from 454 sequencing on short reference sequences. I would like to create a consensus sequence in fasta format from this bam file using R Bioconductor. Is there a way to do that simply ?
Thanks in advance

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] grDevices datasets  splines   graphics  stats     tcltk     utils    
[8] methods   base     

other attached packages:
[1] Rsamtools_1.10.2     Biostrings_2.26.3    GenomicRanges_1.10.7
[4] IRanges_1.16.6       BiocGenerics_0.4.0   TinnR_1.0-5         
[7] R2HTML_2.2.1         Hmisc_3.10-1.1       survival_2.36-14    

loaded via a namespace (and not attached):
[1] bitops_1.0-5    cluster_1.14.4  grid_2.15.1     lattice_0.20-15
[5] parallel_2.15.1 stats4_2.15.1   tools_2.15.1    zlibbioc_1.4.0 

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