function MAF_from_BAM

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Description

Read BAM files and create MAF file. BAMfiles are stored in a sub-folder '/rBAM'. MAF files are intermediate files stored in a sub-folder '/BER'. MAF files contain the raw counts of A,T,C,G, insertion, deletion, insertion>2bp, deletion >2bp for strand plus and stand minus. Note : we strongly recommand to externally recalibrate BAM files using tools like GATK.

Usage

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MAF_from_BAM(study.dir = "Plasma/", input.filenames = NULL,
  bai.ext = ".bai", pos_ranges.file = NULL, force = FALSE)

Arguments

study.dir,

char, name of the folder containing the rBAM directory (default 'Plasma/'). The typical folder hierarchy will consist of 'Plasma/rBAM'

input.filenames,

a vector of char (default NULL), the names of the BAM files to process. If NULL all BAM files in the rBAM folder will be processed

bai.ext,

char, filename extension of the bai files (default '.bai')

pos_ranges.file,

char, name of the Rdata file containing the three variables pos_ind, pos_snp and pos_ranges as build by the function PrepareLibrary. Default NULL, use the position_ranges.rda provided, used for our analysis.

force,

boolean, (default FALSE) if TRUE force all computations to all files including already processed ones

Value

the number of processed bam files

Author(s)

N. P├ęcuchet, P. Laurent-Puig and Y. Rozenholc

References

Analysis of base-position error rate of next-generation sequencing to detect tumor mutations in circulating DNA N. P├ęcuchet, Y. Rozenholc, E. Zonta, D. Pietraz, A. Didelot, P. Combe, L. Gibault, J-B. Bachet, V. Taly, E. Fabre, H. Blons, P. Laurent-Puig in Clinical Chemistry

Examples

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   ## Not run: 
     ctrl.dir = system.file("extdata", "4test_only/ctrl/", package = "PlasmaMutationDetector")
     if (substr(ctrl.dir,nchar(ctrl.dir),nchar(ctrl.dir))!='/')
       ctrl.dir = paste0(ctrl.dir,'/') # TO RUN UNDER WINDOWS
     MAF_from_BAM(ctrl.dir,force=TRUE)
   
## End(Not run)