name: mapdamage2 description: Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. keywords: - ancient DNA - DNA damage - NGS - damage patterns - bam tools: - mapdamage2: description: Tracking and quantifying damage patterns in ancient DNA sequences homepage: http://ginolhac.github.io/mapDamage/ documentation: https://ginolhac.github.io/mapDamage/ tool_dev_url: https://github.com/ginolhac/mapDamage doi: "10.1093/bioinformatics/btt193" licence: ['MIT'] input: - meta: type: map description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.{bam}" - fasta: type: file description: Fasta file, the reference the input BAM was mapped against pattern: "*.{fasta}" output: - meta: type: map description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - runtime_log: type: file description: Log file with a summary of command lines used and timestamps. pattern: "Runtime_log.txt" - fragmisincorporation_plot: type: file description: A pdf file that displays both fragmentation and misincorporation patterns. pattern: "Fragmisincorporation_plot.pdf" - length_plot: type: file description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. pattern: "Length_plot.pdf" - misincorporation: type: file description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. pattern: "misincorporation.txt" - pctot_freq: type: file description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. pattern: "5pCtoT_freq.txt" - pgtoa_freq: type: file description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. pattern: "3pGtoA_freq.txt" - dnacomp: type: file description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. pattern: "dnacomp.txt" - lgdistribution: type: file description: Contains a table with read length distributions per strand. pattern: "lgdistribution.txt" - stats_out_mcmc_hist: type: file description: A MCMC histogram for the damage parameters and log likelihood. pattern: "Stats_out_MCMC_hist.pdf" - stats_out_mcmc_iter: type: file description: Values for the damage parameters and log likelihood in each MCMC iteration. pattern: "Stats_out_MCMC_iter.csv" - stats_out_mcmc_trace: type: file description: A MCMC trace plot for the damage parameters and log likelihood. pattern: "Stats_out_MCMC_trace.pdf" - stats_out_mcmc_iter_summ_stat: type: file description: Summary statistics for the damage parameters estimated posterior distributions. pattern: "Stats_out_MCMC_iter_summ_stat.csv" - stats_out_mcmc_post_pred: type: file description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. pattern: "Stats_out_MCMC_post_pred.pdf" - stats_out_mcmc_correct_prob: type: file description: Position specific probability of a C->T and G->A misincorporation is due to damage. pattern: "Stats_out_MCMC_correct_prob.csv" - dnacomp_genome: type: file description: Contains the global reference genome base composition (computed by seqtk). pattern: "dnacomp_genome.csv" - rescaled: type: file description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. pattern: "*.{bam}" - fasta: type: file description: Allignments in a FASTA file, only if flagged by -d. pattern: "*.{fasta}" - folder: type: folder description: Folder created when --plot-only, --rescale and --stats-only flags are passed. pattern: "*/" authors: - "@darcy220606"