DOKK / manpages / debian 11 / mapdamage / mapDamage.1.en
MAPDAMAGE(1) User Commands MAPDAMAGE(1)

mapDamage - tracking and quantifying damage patterns in ancient DNA sequences

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

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.

show program's version number and exit
show this help message and exit
Input files:
SAM/BAM file, must contain a valid header, use '-' for reading a BAM from stdin
Reference file in FASTA format
General options:
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.
Seed value to use for downsampling. See documentation for py module 'random' for default behavior.
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.
read length, in nucleotides to consider [70]
nucleotides to retrieve before/after reads [10]
minimum base quality Phred score considered, Phred-33 assumed [0]
folder name to store results [results_FILENAME]
Write alignments in a FASTA file
Run only plotting from a valid result folder
Disable any output to stdout
Display progression information during parsing
Override the system wide installed mapDamage module
Options for graphics:
graphical y-axis limit for nucleotide misincorporation frequencies [0.3]
read length, in nucleotides, considered for plotting nucleotide misincorporations [25]
the number of reference nucleotides to consider for plotting base composition in the region located upstream and downstream of every read [10]
title used for plots []
Options for the statistical estimation:
Number of random starting points for the likelihood optimization [30]
Number of burnin iterations [10000]
Number of adjust proposal variance parameters iterations [10]
Number of final MCMC iterations [50000]
Using only the 5' end of the seqs [False]
Using only the 3' end of the seqs [False]
Variable dispersion in the overhangs [False]
Use Jukes Cantor instead of HKY85 [False]
The overhangs are different for 5' and 3' [False]
Fix the nick frequency vector (Only C.T from the 5' end and G.A from the 3' end) [False]
Use the raw nick frequency vector without smoothing [False]
Single stranded protocol [False]
Use black and white theme in post. pred. plot [False]
How long sequence to use from each side [12]
Run only statistical estimation from a valid result folder
Rescale the quality scores in the BAM file using the output from the statistical estimation
Run only rescaling from a valid result folder
Write the rescaled BAM to this file
Disabled statistical estimation, active by default
Check if the R modules are working

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

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

August 2016 mapDamage 2.0.6