Bayesian haplotype-based mutation calling
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Updated
Aug 12, 2023 - C++
Bayesian haplotype-based mutation calling
A python parser to simplify and build the VCF (Variant Call Format).
Segmented HAPlotype Estimation and Imputation Tool
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 Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
Minor Variant Calling and Phasing Tools
ClairS - a deep-learning method for long-read somatic small variant calling
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
An efficient genetic data imputation pipeline
Ploidy agnostic phasing pipeline and algorithm
GWAS QC, PCA, haplotype phasing, genotype imputation
An R interface for 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 Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infe…
Python library for simple and complex indels.
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 correlation), Concordance.
a python program to stitch the ReadBack phased haplotypes in F1 hybrids.
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
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