QuantiSNP

[…] santa clara, california, usa), birdsuite [] and ipattern (j zhang et al., manuscript submitted) were used to call cnvs. for illumina 1 m, the snp calling was done using the beadstudio software. quantisnp [] and ipattern were used to identify cnvs. for both platforms, only variants confirmed by at least two calling algorithms were included in the final set of calls., the agilent custom human […]

[…] would be returned in the same way where the splice junctions would be identified between exons in rna-seq analysis., hapmap project provided a cnv calling report based on snp microarray data using quantisnp [] and birdseye []. the 1000 genome project also provided a dna structural variation report as a vcf file based on nsg data. both reports were published with extra experimental information […]

[…] was claimed under a significance threshold of p-value < 0.05., furthermore, the intensity data of 497,849 snps were used to call the cnv regions. cnvs were identified using penncnv and quantisnp, respectively, which identifies cnvs by integrating intensity data from neighboring probes using a hidden markov model (hmm). gene-based cnvs association analysis was used to test whether […]

[…] hormone receptor (fshr) and the luteinizing hormone/choriogonadotropin receptor (lhcgr), with 61 and 19 snps respectively., we performed cnvs prediction in our dataset using the penncnv and quantisnp algorithms [,]. penncnv was executed using the -test option using default values. quantisnp algorithm was executed enabling the options-isaffy and -levels, since we used an affymetrix […]

[…] populations by powerfully detecting common and rare variants across the 5 most commonly studied subpopulations including african, admixed american, east asian, european, and south asian. using the quantisnp algorithm, 11 and 16 high confidence cnvs (max log bf > 10) were called in two replicates. of these 4 and 5 cnvs respectively met the 50% reciprocal overlapping criteria with a gold […]

[…] of all samples by three standard variation, or with median signal intensity deviating from median signal intensity of all samples by 1.5 interquartile range (iqr) were excluded., penncnv and quantisnp were used for cnv detection with genotype data of illumina microarray chips (omni one for gwas sub-population 1, omni zhonghua for gwas sub-population 3, and 610-quad for gwas […]