schmutzi specifications


Unique identifier OMICS_10291
Name schmutzi
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data text
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Janet Kelso <>

Publication for schmutzi

schmutzi in publications

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

[…] burrows-wheeler-aligner (bwa) []; reads with mapping quality below 30 were discarded and pcr duplicates were removed by rmdup in samtools []. for all samples, a 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 […]

PMCID: 5794802
PMID: 29391530
DOI: 10.1038/s41598-018-20180-z

[…] determined. for this purpose, a complete 395 x coverage mitochondrial genome of george bähr was reconstructed and a quality filtered (q > 30) consensus sequence of his genome was created using schmutzi. his maternal haplogroup was determined to be h35 using haplogrep 2, which is a common subclade of haplogroup h in central europe. furthermore, the y chromosomal haplogroup of george bähr […]

PMCID: 5789860
PMID: 29382937
DOI: 10.1038/s41467-018-02825-9

[…] from further analyses. we evaluated the authenticity of the samples by observing typical patterns of deamination towards read ends (supplementary data ), estimating heterozygosity on the mtdna with schmutzi and heterozygosity on the x chromosome in male samples with angsd (supplementary data ), and evaluating the ratio of the reads mapping to x and y which showed no outliers (see below)., […]

PMCID: 5741722
PMID: 29273718
DOI: 10.1038/s41598-017-18356-0

[…] such extremely high terminal c → t transition rates have only previously been described for archaic hominin mitogenomes (fig. ).figure 3 , modern contamination was estimated using the program schmutzi. for all samples, contamination estimates were low, ranging from 1–6% (table ). at these levels, contamination is unlikely to affect the determination of consensus sequences for high […]

PMCID: 5565772
PMID: 28783727
DOI: 10.1038/nature23310

[…] quality (mapq≥10), sites with a minimum sequencing quality (≥20), and removing two bases at the ends of reads., modern human contamination of the mitochondrial dna was assessed using the software schmutzi which takes into account that the consensus sequence should be reconstructed from reads showing characteristics of ancient dna and originating from a single individual (). we assessed […]

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schmutzi institution(s)
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada

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