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SNPQC specifications


Unique identifier OMICS_30102
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#, R
Database management system SQLite
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Cedric Gondro
  • person_outline Seung Hwan Lee

Publications for SNPQC

SNPQC citations


Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle

PMCID: 5596489
PMID: 28899355
DOI: 10.1186/s12711-017-0342-1

[…] cluded due to population stratification, criteria for genotype data filtering were applied per breed and focused on genotyping quality. Genotypes of the DGEA1 and 2 and SRUC data were filtered using ‘SNPQC’ an R pipeline for quality control of Illumina SNP genotyping array data described in [] to eliminate SNPs that had a median GC score lower than 0.6 and a sample-wise call rate lower than 90%. O […]


Identify latent chromosomal aberrations relevant to myelodysplastic syndromes

Sci Rep
PMCID: 5583229
PMID: 28871208
DOI: 10.1038/s41598-017-10551-3

[…] The data of Cytoscan 750 K Microarray were analyzed using Chromosome Analysis Suite Version 2.0 (Affymetrix). The QC thresholds were: SNPQC ≥ 15.0; MAPD ≤ 0.25; Waviness SD ≤ 0.12. These QC metrics can evaluate the overall quality of SNP array data. Median Absolute Pairwise Difference (MAPD) represents the typical distance between m […]


Genomic markers of ovarian adenocarcinoma and its relevancy to the effectiveness of chemotherapy

PMCID: 5588060
PMID: 28927094
DOI: 10.3892/ol.2017.6590

[…] CEL files were processed using OncoScan Console software, version 1.1.034 (Affymetrix, Inc.), to recalculate probe intensities into genomic landscape (OSCHP file) as well as a set of QC metrics (MAPD SNPQC and waviness). For each sample, a profile of copy number alterations was created, expressed by numerical values. The LOH profile was created for all samples, assuming a high confidence interval […]


Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions

PLoS Curr
PMCID: 5346028
PMID: 28357155
DOI: 10.1371/currents.eogt.7d92ce775800ef3fbc72e3840fb1bc22

[…] cally determined quality control metrics are used that reflect overall data quality on an Affymetrix array: 1) waviness-SD, 2) median of the absolute values of all pairwise differences (MAPD), and 3) SNPQC (measure of how well genotype alleles are resolved). Details regarding these quality control features can be found in the Affymetrix ChAS User Guide ( […]


Report of 5 novel mutations of the α L iduronidase gene and comparison of South Korean mutations in relation with those of Japan or China in patients with mucopolysaccharidosis I

BMC Med Genet
PMCID: 4983032
PMID: 27520059
DOI: 10.1186/s12881-016-0319-x

[…] trix. The quality control (QC) parameters used in our analyses and their definitions and values, which were recommended by Affymetrix, were as follows: Single nucleotide polymorphism quality control (SNPQC: How well the A and B allele can be resolved) ≥15, median of the absolute values of all pairwise differences (MAPD: How similar the signal distribution of the sample is relative to the reference […]


Local and global patterns of admixture and population structure in Iranian native cattle

BMC Genet
PMCID: 4946207
PMID: 27418004
DOI: 10.1186/s12863-016-0416-z

[…] ormed using the Illumina high-density Bovine BeadChip (Illumina, Inc, San Diego, CA, USA) designed to genotype 777,962 SNPs. Quality control of the autosomal genotypes was performed using the program snpQC [] across all Iranian breeds and per outgroup breed. Filtering parameters included a GC score >0.9 (418,571 SNPs failed), call rates per marker >90 % (295,607 SNPs failed) and per animal >70 % ( […]


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SNPQC institution(s)
The Centre for Genetic Analyses and Applications, University of New England, Armidale, NSW, Australia; CSIRO Agriculture, St Lucia, QLD, Australia; Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, Korea
SNPQC funding source(s)
Supported by a grant from the NextGeneration BioGreen 21 Program (No. PJ009954), Rural Development Administration, Republic of Korea and an Australian Research Council Discovery Project DP130100542.

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