mapDamage protocols

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mapDamage specifications

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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
Requirements
gam, python, bedtools, pysam, cython, ggplot2 0.9.2
Maintained Yes

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Publications for mapDamage

mapDamage in pipelines

 (16)
2018
PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750

[…] (https://bitbucket.org/ustenzel/biohazard). reads shorter than 30 base pairs and with mapping quality less than 30 were removed using samtools []. the resulting bam files were processed using mapdamage 2.0 on default settings with plotting and statistical estimation []. haplogrep v2.1.0 [] using phylotree build 17 [] was used to identify the haplogroup of the mtdna as u5a1b. the complete […]

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 mapdamage2.0. 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

[…] 0.098 in males (). 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 […]

2017
PMCID: 5490259
PMID: 28654082
DOI: 10.1038/ncomms15951

[…] and merged mac002 reads were mapped back to our final consensus sequence using bwa and parsed using samtools, allowing investigation of adna damage patterns and read length distributions using mapdamage2.0.2–8 (ref. ; )., we retrospectively mapped reads from the other analysed samples to our final macrauchenia consensus sequence using bwa 0.7.8 (ref. ), to better assess the presence […]

2017
PMCID: 5520058
PMID: 28719574
DOI: 10.1038/ncomms16082

[…] for the x and y chromosomes was ∼5 × for both samples, indicating they were males. mean fragment length for both samples ranged from 60 to 70 bp. postmortem degradation effects were assessed using mapdamage_v1.0 (ref. ), revealing extensive 5′ c>t and 3′ g>a damage. single-ended reads for ngd extracted from a bam file containing all mapped reads were processed using the same pipeline. […]


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mapDamage in publications

 (73)
PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] identified as male (ngd, ctc, and hxh dogs) were aligned to our custom canine reference using the same procedure as described previously [, ]. in short, the damage patterns identified with mapdamage were adjusted into the confidence of the variant calling [, ]. we limited our analysis of ancient samples to positions with a minimum read depth of 4; genotype quality score of 30; map […]

PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] -o $out, where $in is the input bam file and $out is the output bam file., to authenticate adna data sets, we evaluated the presence of postmortem dna damage signatures from read alignments using mapdamage v2.0.6 with default parameters and the following command:, mapdamage -v -i $bam -r $ref -l 100 -d $prefix, where $bam is the input bam file containing only merged reads, $ref […]

PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] using mitos webserver (http://mitos.bioinf.uni-leipzig.de/index.py) and made publicly available (genbank accession number will be inserted here)., ancient dna damage patterns were assessed using mapdamage v2 [], for helminth, vertebrate and plastid identified hits. the analyses were performed as an average of all reads assigned accordingly ( and – tables). for each library the 5’ c […]

PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] probabilistic iterative approach, schmutzi [], was used to call the endogenous consensus sequences and to estimate the contamination levels. misincorporation patterns were tracked and quantified by mapdamage 2.0 []. the latter one was also executed for the reconstruction of endogenous mitochondrial genomes. classification of complete mtdna sequences according to haplogroup nomenclature […]

PMCID: 5879695
PMID: 29531040
DOI: 10.1073/pnas.1719880115

[…] were processed as described previously (). haploid and diploid genotype calling was performed, accounting for postmortem damage as previously described ()., postmortem damage was assessed using mapdamage 2.0 (). contamination was estimated from the mitochondrial capture data using the approach of fu et al. () and for all male shotgun data using angsd () (si appendix, section 8 and table […]


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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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