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SNPolisher specifications


Unique identifier OMICS_05205
Name SNPolisher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


SNPolisher citations


Genetic analysis of Japanese primary open angle glaucoma patients and clinical characterization of risk alleles near CDKN2B AS1, SIX6 and GAS7

PLoS One
PMCID: 5737967
PMID: 29261660
DOI: 10.1371/journal.pone.0186678
call_split See protocol

[…] E2, and considered a SNP with info score great than 0.9 as an acceptable well-imputed variant in this study. Autosomal SNPs that were assigned to ‘Recommended’ by the Ps_Classification program in the SNPolisher package (Affymetrix) were selected. We applied the following thresholds for quality control in further data cleaning: Hardy–Weinberg equilibrium with a P value <1.00E-04 for control samples […]


Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome

Plant Biotechnol J
PMCID: 5814592
PMID: 28921769
DOI: 10.1111/pbi.12831

[…] the manufacturer's instructions (Axiom 2.0 Assay Manual Workflow User Guide Rev3). Allele designation was performed with the Affymetrix proprietary software packages Affymetrix Power Tools (APT) and SNPolisher™ (, and for genotyping ‘Z1842’, ‘Z2098’ and their 119 progeny, a custom software pipeline ADAP ( […]


Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

PLoS One
PMCID: 5628821
PMID: 28981529
DOI: 10.1371/journal.pone.0185220

[…] Array.Quality control (QC) on genotypes discarded replicated individuals and those with call rate (CR) lower than 10%. Only the best quality SNP probe category “PolyHighRes” called by the Affymetrix’ SNPolisher R package were retained and SNPs with a minor allele frequency (MAF) and a CR lower than 1% and 10% respectively were rejected. Preliminary analysis of the genetic structure of the populati […]


Pharmacogenetic meta analysis of baseline risk factors, pharmacodynamic, efficacy and tolerability endpoints from two large global cardiovascular outcomes trials for darapladib

PLoS One
PMCID: 5533343
PMID: 28753643
DOI: 10.1371/journal.pone.0182115
call_split See protocol

[…] 5%, were monomorphic or if Hardy-Weinberg p-values were less than 10−6 in White and Korean subgroups. When a variant had multiple markers on the array the best assay was included using the Affymetrix SNPolisher Best Probeset filter ( SOLID-TIMI 52 genotype data was generated by BPS for 35 candid […]


Molecular Genetic Influences on Normative and Problematic Alcohol Use in a Population Based Sample of College Students

Front Genet
PMCID: 5350109
PMID: 28360924
DOI: 10.3389/fgene.2017.00030
call_split See protocol

[…] 96 k) for imputation and functional variants (357 k) including rare high impact exome variants (272 k), indels (18 k), eQTLs (16 k), and miscellaneous (51 k). QC excluded Off Target Variants found by SNPolisher, single nucleotide polymorphisms (SNPs) missing >5% of genotypes, samples missing >2% of genotypes, and SNPs missing >2% of genotypes after sample filtering, similar to the Psychiatric Geno […]


A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum

Plant Biotechnol J
PMCID: 5258861
PMID: 27459228
DOI: 10.1111/pbi.12606

[…] rocedure described by Affymetrix (Axiom® 2.0 Assay Manual Workflow User Guide Rev3). Allele calling was carried out using the Affymetrix proprietary software packages Affymetrix Power Tools (APT) and SNPolisher™ ( A custom software pipeline ADAP (Axiom® Data Analysis Pipeline) was written in perl to simpl […]


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