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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, or


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