mapDamage protocols

mapDamage specifications

Information


Unique identifier OMICS_02099
Name mapDamage
Alternative name mapDamage2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Publications for mapDamage

mapDamage IN pipelines

 (7)
2017
PMCID: 5335606
PMID: 28256601
DOI: 10.1038/srep42869

[…] reads with mapping quality below 30 were discarded and pcr duplicates were collapsed into consensus sequences. to estimate the misincorporation pattern at the end of the reads, bam files were run on mapdamage2.072. then, to test for the authenticity of the consensus sequences, we used a bayesian contamination estimate to calculate the probability that the recovered mtdna fragments come […]

2017
PMCID: 5483232
PMID: 28552360
DOI: 10.1016/j.cub.2017.05.023

[…] males (table s2). all samples could be assigned to one of the two sexes with confidence higher than 95%, and all the genetic assignments were consistent with morphological identifications., we used mapdamage to rescale the base quality score of t and a according to their probability of resulting from molecular damage (c to u deaminations). we used these rescaled bam files and samtools mpileup […]

2016
PMCID: 4880306
PMID: 27224451
DOI: 10.1371/journal.pone.0155046

[…] pcr duplicates were also removed from the unmerged reads using picard’s markduplicates tool (http://broadinstitute.github.io/picard/). to confirm the authenticity of our ancient dna, the program mapdamage (v2.0.2–9) [22] which identifies characteristic adna damage patterns, was used with the '-rescale' option to lower the quality score of likely damaged sites. the plots of characteristic […]

2016
PMCID: 5121605
PMID: 27881876
DOI: 10.1038/srep37347

[…] a minimum mapping quality score (mapq) of 25. duplicates were removed with markduplicates from picard tools v.1.96 (http://picard.sourceforge.net/). finally, we obtained adna damage patterns using mapdamage v.2.0.66061 for reads from all libraries mapped to each of the four genomes (i.e. from four bam files per library). after observing adna damage patterns in several libraries when mapped […]

2015
PMCID: 4472748
PMID: 26086078
DOI: 10.1371/journal.pone.0129102

[…] and filtering for reads with a minimum qc score of 30, indicating 99.9% base call accuracy. samtools v0.1.19-96b5f2294a [32] was used to remove duplicates. damage patterns were assessed using the mapdamage tool [33] and normalized contamination estimates were calculated as in gamba et al. [8], we found substantial difference in both endogenous content and total endogenous dna yields […]

mapDamage institution(s)
Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen University, Denmark
mapDamage funding source(s)
Danish Council for Independent Research; Natural Sciences (FNU); Danish National Research Foundation (Danmarks Grundforskningsfond)

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