mapDamage - tracking and quantifying damage patterns in ancient DNA sequences

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

mapDamage 2.0.6                                    August 2016                                      MAPDAMAGE(1)

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

       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.

       mapDamage - tracking and quantifying damage patterns in ancient DNA sequences

--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

mapDamage [options] -iBAMfile-rreference.fasta