low-coverage-sequencing

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Genotype imputation pipelines for the UK Biobank Research Analysis Platform

Imputation workflow for low coverage whole genome sequencing data

This is the official development repository for BaseVar, which call variants for large-scale ultra low-depth(<1.0x) WGS data, especially for NIPT data and ancient DNA

The repo was not under active development. Check out angsd toolkit for low depth data analyses.

Imputation and Admixture for lcWGS in one goal

Two Nextflow pipelines for mapping and imputation of non-human samples sequenced at low-coverage.

Supporting data for the publication "Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients"

A pipeline to call SNPs, and SV from low coverage WGRS data

LCVCFtools is a program designed for working with VCF files generated from low-coverage whole genome sequencing

Asses the validity of imputation of your low-coverage samples

fastlckin: A high-performance C++17 tool for maximum likelihood kinship estimation from low-coverage sequencing data using genotype likelihoods.

This repository contains scripts for NYC oyster admixture project