MAF_from_BAM {PlasmaMutationDetector2}

function MAF_from_BAM

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

MAF_from_BAM(
  study.dir = "Plasma/",
  input.filenames = NULL,
  bai.ext = ".bai",
  pos_ranges.file = NULL,
  force = FALSE,
  output.dir = study.dir,
  n.trim = 8
)

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

output.dir

char, name of the folder to save results (default study.dir)

n.trim

integer, number of base positions trimmed at the ends of each amplicon (default 8)

Value

the path/names of the MAF files

Author(s)

N. Pécuchet, P. Laurent-Puig, O. Nordgård and Y. Rozenholc

References

Analysis of base-position error rate of next-generation sequencing to detect tumor mutations in circulating DNA N. Pécuchet, 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

Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund Nordgård in Scientific Reports

Examples

  ## Not run: 
     ctrl.dir = system.file("extdata", "4test_only/ctrl/",
       package = "PlasmaMutationDetector2")
     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,output.dir=paste0(tempdir(),'/'))
   
## End(Not run)