DamageProfiler

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, James A. Fellows Yates, and Alexander Hübner.

Citation

If you use the tool, please cite the publication:

DamageProfiler Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. Bioinformatics (btab190). https://doi.org/10.1093/bioinformatics/btab190

Method

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

It creates

• damage plots
• fragment length distribution
• read identity distribution
• base frequency table of reference
• table of different base misincorporations and their occurrences

How to run

java -jar DamageProfiler-VERSION.jar -i input_file -o output_folder [options]

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

-h, —help\
Shows this help page.\
\
-v, —version\
Shows the version of DamageProfiler.\
\
-i INPUT\
The input sam/bam/cram file (Required).\
\
-o OUTPUT\
The output folder (Required).\
\
-r REFERENCE\
The reference file (fasta format).\
\
-t THRESHOLD\
DamagePlot: Number of bases which are considered for plotting nucleotide misincorporations. Default: 25.\
\
-s SPECIES\
Reference sequence name (Reference sequence name (SN tag) of the SAM record). Species must be put in
quotation marks (e.g. -s ‘NC032001.1|tax|1917232|’), multiple species must be comma separated
(e.g. -s ‘NC_032001.1|tax|1917232|,NC_031076.1|tax|1838137|,NC_034267.1|tax|1849328|’). Commas within the reference
sequence name are not allowed. Please specify either -s or -sf.\
\
-sf FILE SPECIES\
Text file containing a list with species (Reference sequence name (SN tag) of the SAM record, one per line) for which
damage profile has to be calculated. Please specify either -s or -sf.\
\
-l LENGTH\
Number of bases which are considered for frequency computations. Default: 100.\
\
-title TITLE\
Title used for all plots. Default: input filename.\
\
-yaxis_dp_max MAX_VALUE\
DamagePlot: Maximal y-axis value.\
\
-color_c_t COLOR_C_T\
DamagePlot: Color (HEX code) for C to T misincorporation frequency.\
\
-color_g_a COLOR_G_A\
DamagePlot: Color (HEX code) for G to A misincorporation frequency.\
\
-color_insertions COLOR_C_T\
DamagePlot: Color (HEX code) for base insertions.\
\
-color_deletions COLOR_DELETIONS\
DamagePlot: Color (HEX code) for base deletions.\
\
-color_other COLOR_OTHER\
DamagePlot: Color (HEX code) for other bases different to reference.\
\
-only_merged\
Use only mapped and merged (in case of paired-end sequencing) reads to calculate damage plot instead of using all mapped reads. The SAM/BAM entry must start with ‘M‘, otherwise it will be skipped. Default: false.\
\
-sslib\
Single-stranded library protocol was used. Default: false.

A more detailed documentation of DamageProfiler is available at
https://damageprofiler.readthedocs.io.