phasing topic
octopus
Bayesian haplotype-based mutation calling
princess
SubPhaser
Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
VCF-Simplify
A python parser to simplify and build the VCF (Variant Call Format).
minorseq
Minor Variant Calling and Phasing Tools
nPhase
Ploidy agnostic phasing pipeline and algorithm
shapeit5
Segmented HAPlotype Estimation and Imputation Tool
ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
rd-imputation-accuracy
Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correl...
DEploid
dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Marko...