SNPest protocols

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SNPest statistics

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SNPest specifications

Information


Unique identifier OMICS_08845
Name SNPest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data SNPest takes input generated by the “samtools mpileup -s” command (or equivalent) reporting nucleotides mapped to each position together with read qualities and mapping qualities.
Output data The output is in VCF format with a line per position covered in the genome.
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Stinus Lindgreen <>

Publications for SNPest

SNPest in pipeline

2017
PMCID: 5686521
PMID: 29152586
DOI: 10.1128/mSystems.00127-17

[…] with default parameters (). the bam files were processed using samtools (-q 25 -q 0) to generate mpileup output (). this output was used to create high-confidence genotypes for each strain using snpest v. 1.0 (minimum depth of 10 reads, minimum posterior probability of 0.999, minimum support for indel of 90%) (). the reference embl file was processed using an in-house script to extract […]


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SNPest in publications

 (2)
PMCID: 5686521
PMID: 29152586
DOI: 10.1128/mSystems.00127-17

[…] with default parameters (). the bam files were processed using samtools (-q 25 -q 0) to generate mpileup output (). this output was used to create high-confidence genotypes for each strain using snpest v. 1.0 (minimum depth of 10 reads, minimum posterior probability of 0.999, minimum support for indel of 90%) (). the reference embl file was processed using an in-house script to extract […]

PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] or only for mtdna. such algorithms report the probabilities of different types of postmortem dna degradation, which allows for better statistical modelling at the variant calling stage, employing snpest or custom scripts. a typical ngs pipeline for adna analysis is shown in . figure 3. , the amount of extracted endogenous dna may allow satisfactory coverage of adna sequences (as high […]


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SNPest institution(s)
Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej, Copenhagen, Denmark

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