genotype-likelihoods
There are 19 repositories under genotype-likelihoods topic.
thierrygosselin/radiator
RADseq Data Exploration, Manipulation and Visualization using R
fgvieira/ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
grenaud/glactools
command-line tools for the management of genotype likelihoods and allele counts
thierrygosselin/stackr
stackr: an R package to run stacks software pipeline
lvclark/polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
clemgoub/TypeTE
Genotyping of segregating mobile elements insertions
fgvieira/ngsF
Estimation of per-individual inbreeding coefficients under a probabilistic framework
pblischak/polyploid-genotyping
SNP genotyping in polyploids
SamueleSoraggi/HMMploidy
A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models
ANGSD-wrapper/angsd-wrapper
Utilities for analyzing next generation sequencing data.
fgvieira/ngsF-HMM
Estimation of per-individual inbreeding tracts under a probabilistic framework
fgvieira/ngsDist
Estimation of pairwise distances under a probabilistic framework
isinaltinkaya/vcfgl
Genotype likelihood simulator for VCF/BCF files
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.
zhangyi-he/WFM-1L-DiffusApprox-PMMH
Estimating temporally variable selection intensity from ancient DNA data
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
jhidalgo-lopez/SNP-Clustering
Perl software to cluster SNPs based on its genotype.
zhangyi-he/WFM-2L-DiffusApprox-AdaptPMMH
Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis
adiamb/IMPUTE-PIPELINE-MIGNOT-LAB
A pipeline to impute plink genotypes to 1000 Genomes phase 1