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Quantisnp
...dden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research, 35(6):2013-2025 2007.]

2 KB (297 words) - 20:29, 12 August 2022
KING
KING is a toolset making use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequenci

3 KB (305 words) - 19:28, 12 August 2022
NextGenMap
...of runtime. This allows analyzing large-scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protoc

3 KB (309 words) - 16:24, 19 August 2022
FreeBayes
...predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heteroge

2 KB (302 words) - 18:55, 12 August 2022
Wgsim
One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl

3 KB (343 words) - 21:29, 6 December 2019
SOLAR
...nents analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations ar

3 KB (328 words) - 21:24, 6 December 2019
FcGENE
...ata such as PLINK and MACH. The usage is two-fold. First, convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BE

3 KB (326 words) - 16:38, 15 August 2022
PolyGembler
...sumes availability of genome-wide genotyping data such as GBS, RAD-seq and SNP array data, collected on a F1 outbred mapping population, as well as high c

3 KB (344 words) - 13:45, 3 November 2020
Dadi
...he joint demographic history of multiple populations from multidimensional SNP data" PLoS Genetics 5:e1000695 (2009).

3 KB (350 words) - 21:21, 6 December 2019
RGI
...predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses reference data from the Comprehensive Antibiot

3 KB (352 words) - 21:24, 6 December 2019
Ngstools
...ical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth * SNP calling, genotype calling, and sample allele frequency estimation from New-

5 KB (708 words) - 15:31, 14 December 2022
Nanocaller
...aller uses long-range haplotype structure to generate predictions for each SNP candidate variant site by considering pileup information of other candidate

3 KB (351 words) - 15:41, 16 March 2023
ADMIXTURE
...for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calc

3 KB (366 words) - 20:51, 11 August 2022
Samtools
Bcftools does the SNP calling. It can also concatenate BCF files, index BCFs for fast random acce

3 KB (357 words) - 22:04, 21 August 2022
Deepvariant
A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechno

3 KB (356 words) - 13:17, 16 April 2024
PGDSpider
...ograms for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Be

3 KB (387 words) - 19:04, 10 June 2022
SMR
...hodology can be interpreted as an analysis to test if the effect size of a SNP on the phenotype is mediated by gene expression. This tool can therefore be

3 KB (362 words) - 18:27, 19 August 2021
ProbABEL
ProbABEL software package is used for the analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes under linear, l

3 KB (371 words) - 19:35, 21 August 2022
SHEsisPlus
...nbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 2008 Jul 30;9:35

3 KB (344 words) - 15:04, 19 August 2022
Snp2hla
...med/24698974 Pillai NE et al. "Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations." Hum Mol Genet, [epub ahead of p

3 KB (379 words) - 20:42, 12 August 2022

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