NAME

       mapDamage - tracking and quantifying damage patterns in ancient DNA sequences

SYNOPSIS

       mapDamage [options] -i BAMfile -r reference.fasta

DESCRIPTION

       MapDamage  is  a  computational  framework  written  in  Python  and  R,  which tracks and
       quantifies DNA damage patterns among ancient  DNA  sequencing  reads  generated  by  Next-
       Generation Sequencing platforms.

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

              Input files:

       -i FILENAME, --input=FILENAME
              SAM/BAM file, must contain a valid header, use '-' for reading a BAM from stdin

       -r REF, --reference=REF
              Reference file in FASTA format

              General options:

       -n DOWNSAMPLE, --downsample=DOWNSAMPLE
              Downsample to a randomly selected fraction of the reads (if 0 < DOWNSAMPLE < 1), or
              a fixed number of randomly selected reads (if DOWNSAMPLE  >=  1).  By  default,  no
              downsampling is performed.

       --downsample-seed=DOWNSAMPLE_SEED
              Seed  value  to  use for downsampling. See documentation for py module 'random' for
              default behavior.

       --merge-reference-sequences
              Ignore referece sequence names when tabulating reads (using  '*'  instead).  Useful
              for  alignments  with  a  large  number  of reference sequnces, which may otherwise
              result in excessive memory or disk usage due to the number of tables generated.

       -l LENGTH, --length=LENGTH
              read length, in nucleotides to consider [70]

       -a AROUND, --around=AROUND
              nucleotides to retrieve before/after reads [10]

       -Q MINQUAL, --min-basequal=MINQUAL
              minimum base quality Phred score considered, Phred-33 assumed [0]

       -d FOLDER, --folder=FOLDER
              folder name to store results [results_FILENAME]

       -f, --fasta
              Write alignments in a FASTA file

       --plot-only
              Run only plotting from a valid result folder

       -q, --quiet
              Disable any output to stdout

       -v, --verbose
              Display progression information during parsing

       --mapdamage-modules=MAPDAMAGE_MODULES
              Override the system wide installed mapDamage module

              Options for graphics:

       -y YMAX, --ymax=YMAX
              graphical y-axis limit for nucleotide misincorporation frequencies [0.3]

       -m READPLOT, --readplot=READPLOT
              read length, in nucleotides, considered for plotting  nucleotide  misincorporations
              [25]

       -b REFPLOT, --refplot=REFPLOT
              the  number  of  reference nucleotides to consider for plotting base composition in
              the region located upstream and downstream of every read [10]

       -t TITLE, --title=TITLE
              title used for plots []

              Options for the statistical estimation:

       --rand=RAND
              Number of random starting points for the likelihood optimization  [30]

       --burn=BURN
              Number of burnin iterations  [10000]

       --adjust=ADJUST
              Number of adjust proposal variance parameters iterations  [10]

       --iter=ITER
              Number of final MCMC iterations  [50000]

       --forward
              Using only the 5' end of the seqs  [False]

       --reverse
              Using only the 3' end of the seqs  [False]

       --var-disp
              Variable dispersion in the overhangs  [False]

       --jukes-cantor
              Use Jukes Cantor instead of HKY85  [False]

       --diff-hangs
              The overhangs are different for 5' and 3'  [False]

       --fix-nicks
              Fix the nick frequency vector (Only C.T from the 5' end and G.A from  the  3'  end)
              [False]

       --use-raw-nick-freq
              Use the raw nick frequency vector without smoothing [False]

       --single-stranded
              Single stranded protocol [False]

       --theme-bw
              Use black and white theme in post. pred. plot [False]

       --seq-length=SEQ_LENGTH
              How long sequence to use from each side [12]

       --stats-only
              Run only statistical estimation from a valid result folder

       --rescale
              Rescale  the  quality  scores in the BAM file using the output from the statistical
              estimation

       --rescale-only
              Run only rescaling from a valid result folder

       --rescale-out=RESCALE_OUT
              Write the rescaled BAM to this file

       --no-stats
              Disabled statistical estimation, active by default

       --check-R-packages
              Check if the R modules are working

BUGS

       Report bugs to aginolhac@snm.ku.dk, MSchubert@snm.ku.dk or jonsson.hakon@gmail.com

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.