SNPGenie statistics

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SNPGenie specifications


Unique identifier OMICS_10421
Name SNPGenie
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference sequence(s) (.FASTA), a Gene Transfer Format (.GTF) file with CDS annotations and an arbitrary number of SNP reports, currently including Geneious (Variations/SNPs Annotations Table) and CLC Genomics Workbench (Annotated Variant File) formats.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes


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  • person_outline Chase W. Nelson <>

Publication for SNPGenie

SNPGenie in publications

PMCID: 5533922
PMID: 28592544
DOI: 10.1128/JVI.00690-17

[…] points in at least two independent lineages. all of the snps and their frequencies in all of the samples are shown in data set s3 in the supplemental material., snp data were used as an input for snpgenie software (), which was used to calculate the diversity indices for each population. the consensus sequence of the source inoculum sample was used as a reference. average whole-genome […]

PMCID: 5498103
PMID: 28695208
DOI: 10.1126/sciadv.1700239

[…] for recombination rate (). to infer short insertions and deletions, we screened the mapping profiles of each strain and validated each candidate insertion and deletion by polymerase chain reaction. snpgenie (version () was used to infer the number of nonsynonymous and synonymous sites in the coding regions of the o. tauri rcc4221 genome (table s2). vcftools () and a set […]

PMCID: 4898808
PMID: 27189991
DOI: 10.1093/gbe/evw094

[…] bcftools ( using default settings for polyploid organisms., the classic population genetics statistic π () was computed based on the estimated minor allele frequencies using snpgenie (). the folded site frequency spectrum (sfs) estimations were done using several methods. pool-hmm () was run to calculate the allele frequency in our data (option -spectrum) directly […]

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SNPGenie institution(s)
Department of Biological Sciences, University of South Carolina, Columbia, SC, USA; Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, USA

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