A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
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README.md

DamageProfiler

Build Status Documentation Status DOI install with bioconda

This method can be used to calculate damage profiles of mapped ancient DNA reads.

Main author: Judith Neukamm judith.neukamm@uzh.ch Contributor: Alexander Peltzer alexander.peltzer@qbic.uni-tuebingen.de

Method

DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.

It creates

  • damage plots
  • a fragment length distribution
  • a read identity distribution
  • a base frequency table of reference
  • a table of different base misincorporations and their occurrences
How to run
java -jar DamageProfiler-VERSION.jar <arguments> [options]

Arguments:

-h,--help
Shows this help page.

-i,--input
The input sam/bam file.

-o,--output
The output folder

Options:

-l,--length
Number of bases which are computations.

-mapped,--all_mapped_reads
Use all mapped reads to calculate damage plots. Default: false.

-r,--reference
The reference file

-s,--specie
RefSeq ID of the reference genome. This will just use the reads mapping to the specific reference for creating the damage profile. It can for example be used for MALT output files. In this case, please make sure that you run MALT without --sparseSAM option. This would create a sam file with is not readable.
Example: -s NC_022116.1

-sf,--specieslist file
List with species (RefSeq IDs) for which damage profile has to be calculated. One species per line, given as text file (.txt). Species must have the same format like -s parameter.

-t,--threshold
Number of bases which are considered for plotting nucleotide misincorporations.

-title,--title <TITLE>
Title used for all plots (Default: file name of input SAM/BAM file).

-yaxis,--yaxis
Maximal value on y axis (Default: flexible, adapts to the calculated damage).

Running the jar file without any parameter starts a GUI to configure the run.

A more detailed description, manual and tutorial of DamageProfiler is available on https://damageprofiler.readthedocs.io