Pipeline for genotype phasing using SHAPEIT4
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Updated
Mar 24, 2023 - Nextflow
Pipeline for genotype phasing using SHAPEIT4
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…
Step-by-step guide to different types of phasing and testing their accuracy
This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.
A pipeline to select the best K (number of clusters) for fastPHASE imputation and phasing.
Scripts to automate the phasing with several tools
Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.
Microsatellite genotyping
A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.
Autoencoders for genomic data compression, classification, imputation, phasing and simulation.
haplotype estimation, custom panel creation, and genotype imputation
gwas workflow from raw intensity data to in-silico functional mapping
Easy, fast, configurable version of phasor. Perfect for students who what to start with analyzing Coherent X-ray Diffraction Data.
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
a python program to stitch the ReadBack phased haplotypes in F1 hybrids.
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