• PennCNV

  • Referenced in 16 articles [sw19390]
  • copy number variation detection in whole-genome SNP genotyping data. Comprehensive identification and cataloging ... detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources ... intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs ... fine-mapping of CNVs via high-density SNP genotyping. The PennCNV software is available from...
  • Samtools

  • Referenced in 22 articles [sw14583]
  • BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering summarising SNP and short indel sequence variants. HTSlib...
  • GCTA

  • Referenced in 22 articles [sw23135]
  • than testing the association of any particular SNP to the trait. We introduce GCTA...
  • pi-MASS

  • Referenced in 20 articles [sw17249]
  • predictive performance compared with standard single-SNP analyses and the penalized regression method LASSO. Methods...
  • GATK

  • Referenced in 17 articles [sw12019]
  • like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming...
  • GWAS Catalog

  • Referenced in 15 articles [sw41505]
  • searchable, visualisable and freely available database of SNP-trait associations, which can be easily integrated...
  • SNPHarvester

  • Referenced in 6 articles [sw35289]
  • complex diseases. However, existing methods for SNP interaction discovery either suffer from high computation complexity ... propose a new method SNPHarvester to detect SNPSNP interactions in GWA studies. SNPHarvester creates ... multiple paths in which the visited SNP groups tend to be statistically associated with diseases ... then harvests those significant SNP groups which pass the statistical tests. It greatly reduces...
  • BRLMM

  • Referenced in 8 articles [sw11309]
  • program for making genotype calls from Affymetrix SNP microarrays. It currently implements three different genotype ... Currently requires seed genotypes for every SNP and sample analyzed which it obtains...
  • VanillaICE

  • Referenced in 6 articles [sw11310]
  • characterizing chromosomal alterations in high throughput SNP arrays. Background (http://www.biostat.jhsph.edu/ iruczins/software/vanillaice.html): High density single ... nucleotide polymorphism microarrays (SNP chips) provide information on a subject’s genome, such ... fluorescence in situ hybridization and karyotyping, SNP chips provide a high resolution ... diseases are linked to such chromosomal alterations, SNP chips promise new insights for these diseases...
  • IMPUTE

  • Referenced in 11 articles [sw14375]
  • program for estimating (”imputing”) unobserved genotypes in SNP association studies. The program is designed...
  • dChipSNP

  • Referenced in 6 articles [sw18745]
  • dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity. Motivation: Oligonucleotide microarrays ... Here, we report automated methods for pooling SNP array replicates to make LOH calls, visualizing ... SNP and LOH data along chromosomes in the context of genes and cytobands, making statistical...
  • PLASQ

  • Referenced in 6 articles [sw18746]
  • determine allelic dosage in cancer cells from SNP array data. Human cancer is largely driven ... cancer cells from single-nucleotide polymorphism (SNP) microarray data. Our approach is based upon ... cancer samples (e.g., CCCCT at an amplified SNP). Our approach is illustrated on a variety...
  • SSAHA

  • Referenced in 10 articles [sw17308]
  • used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly...
  • ProbABEL

  • Referenced in 6 articles [sw10861]
  • complex traits. Currently, imputed single nucleotide polymorphisms (SNP) data are frequently used in GWA analyzes ... analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes...
  • SimPed

  • Referenced in 5 articles [sw15080]
  • pedigree structures. With the widespread availability of SNP genotype data, there is great interest ... physical distance; however, for dense maps of SNP markers, there can be strong linkage disequilibrium ... being carried out using dense maps of SNP marker loci. Monte Carlo methods are often...
  • HapBlock

  • Referenced in 5 articles [sw26434]
  • HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming ... programs for haplotype block partitioning and tag SNP selection, our program has several notable features ... measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program...
  • GenoSNP

  • Referenced in 4 articles [sw34351]
  • GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference ... intensity data on a single nucleotide polymorphism (SNP) by SNP basis. This approach assumes ... array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium ... SNP genotyping assay that is entirely within-sample and does not require the need...
  • VarScan

  • Referenced in 8 articles [sw27471]
  • lets VarScan run on any operating system. SNP, indel, and consensus calling. In addition...
  • SKAT

  • Referenced in 4 articles [sw26433]
  • package SKAT: SNP-Set (Sequence) Kernel Association Test. Functions for kernel-regression-based association tests ... SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently ... compute SNP-set level p-values...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • SNPs3D: Candidate gene and SNP selection for association studies. Background: The relationship between disease susceptibility ... response and hypertension. Conclusion: The combination of SNP impact analysis, a knowledge based network...