---
name: "mapDamage"
section: "1"
platform: "linux"
package: "mapdamage"
version: "2.2.2+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mapDamage"
---

# mapDamage(1)

tracking and quantifying damage patterns in ancient DNA sequences

## 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.