Man page - mapdamage(1)

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Package:  mapdamage
apt-get install mapdamage

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Manual

MAPDAMAGE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
BUGS
AUTHOR

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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.

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