genotype-likelihoods

There are 2 repositories under genotype-likelihoods topic.

thierrygosselin / radiator
RADseq Data Exploration, Manipulation and Visualization using R
radseq radseq-data imputation genotype-likelihoods filter genetics missingness outliers genomics genomic-data-analysis genomics-visualization gbs genotyping-by-sequencing visualization outliers-detection heterozygosity paralogs artifacts-detection batch-effects normalization
Language:HTML 57
fgvieira / ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
ld genotype-likelihoods population-genomics ngs
Language:C++ 40
grenaud / glactools
command-line tools for the management of genotype likelihoods and allele counts
allele-counts genotype-likelihoods population acf glf genome-wide-data
Language:C++ 28
thierrygosselin / stackr
stackr: an R package to run stacks software pipeline
radseq rad genotype-likelihoods filter genetics genomics genomic-data-analysis genomics-visualization radseq-data gbs genotyping-by-sequencing stackr
Language:R 27
polyRAD
lvclark / polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
bioinformatics r dna-sequencing genotyping-by-sequencing genotype-likelihoods rad-seq rad-sequencing snp-genotyping hacktoberfest
Language:HTML 24
clemgoub / TypeTE
Genotyping of segregating mobile elements insertions
bioinformatics vcf genotyping genotype-likelihoods transposons alu short-reads transposable-elements
Language:Perl 19
fgvieira / ngsF
Estimation of per-individual inbreeding coefficients under a probabilistic framework
population-genomics inbreeding ngs genotype-likelihoods
Language:C 19
SamueleSoraggi / HMMploidy
A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models
genotype-likelihoods alleles ploidy-level allele-counts ploidy-numbers
Language:R 17
pblischak / polyploid-genotyping
SNP genotyping in polyploids
snp-genotyping bioinformatics population-genetics manuscript cpp11 genotype-likelihoods rcpp
Language:C++ 15
ANGSD-wrapper / angsd-wrapper
Utilities for analyzing next generation sequencing data.
software ngs-analysis ngs visualization gui r bash shell wrapper population-genetics next-generation-sequencing sfs bam-files fasta genotype-likelihoods thetas inbreeding-coefficient admixture user-friendly
Language:Shell 14
fgvieira / ngsF-HMM
Estimation of per-individual inbreeding tracts under a probabilistic framework
population-genomics inbreeding ngs genotype-likelihoods hmm
Language:C++ 13
fgvieira / ngsDist
Estimation of pairwise distances under a probabilistic framework
population-genomics genetic-distances ngs genotype-likelihoods
Language:C++ 10
isinaltinkaya / vcfgl
Genotype likelihood simulator for VCF/BCF files
genotype-likelihoods msprime simulation tskit vcf vcf-files
Language:C++ 7
zjnolen / PopGLen
Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.
snakemake bioinformatics bioinformatics-pipeline genotype-likelihoods population-genomics whole-genome-sequencing museomics angsd
Language:Python 4
zhangyi-he / WFM-1L-DiffusApprox-PMMH
Estimating temporally variable selection intensity from ancient DNA data
population-genetics genotype-likelihoods natural-selection hmm diffusion-approximation pmmh wright-fisher-model adna time-series-data
Language:R 1
zhangyi-he / WFM-1L-DiffusApprox-PMMHwGibbs
Estimating temporally variable selection intensity from ancient DNA data with a combination of forward- and backward-in-time simulations
population-genetics genotype-likelihoods natural-selection hmm adna diffusion-approximation wright-fisher-model pmmh time-series-data
Language:R 1
jhidalgo-lopez / SNP-Clustering
Perl software to cluster SNPs based on its genotype.
snp perl genotyping genotype-likelihoods genotypes genotype
Language:Perl 0
zhangyi-he / WFM-2L-DiffusApprox-AdaptPMMH
Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis
genetic-linkage genotype-likelihoods natural-selection population-genetics epistatic-interaction hmm diffusion-approximation wright-fisher-model adna pmmh time-series-data
Language:R 0
adiamb / IMPUTE-PIPELINE-MIGNOT-LAB
A pipeline to impute plink genotypes to 1000 Genomes phase 1
plink-files impute-algorithm scg4 genotype-likelihoods
Language:Shell