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admixture_in_africa

analysis and plotting code for "Admixture into and within Africa" by George Busby et al 2016 (eLife)

badmixture

R package for comparing mixture solutions to similarity data, with a focus STRUCTURE like models to ChromoPainter palettes

bashrc

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bcftools-cheat-sheet

bedtools-protocols

benchmark-germline-variants-prioritizers

Benchmarking of causal germline variant prioritizers

benchmarking

Benchmarking of WGS and WES workflows from NGS reference data and reference samples sequenced at ITER

brca-exchange

Overall management and deployment of the BRCA Exchange web portal and pipeline scripts

broad-prod-wgs-germline-snps-indels

Workflows used in production at Broad for germline short variant discovery in WGS data

checkvcf

Sanity check Variant Call Format (VCF) files.

chronqc

Manuscript describing ChronQC is now available online in Bioinformatics

cmplot

📊 Circular and Rectangular Manhattan Plot

contaminationx

testing new contamination method

covid-19

A public repository of scientific and media resources of SARS-CoV-2 related COVID-19

cruk-bioinf-sschool

http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool

dataharmonizer

docker

exome

A complete pipeline for cohort-oriented exome processing and annotation.

fangli359.github.io

fast-sg

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

fpfilter

A VCF filter for WGS data to filter FPs without losing too many TPs

fraposa

gatk-calling-tests

Statistical tests performed by GATK on the variant calling

gatk-gvcf-header

Description of a typical gVCF

gatk-whole-genome-pipeline

End to end pipeline for calling variants against an entire genome

genome-data-integration

Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls

genomescope

Fast genome analysis from unassembled short reads

genomicsiter.github.io

Test

gwasurvivr

GWAS Survival Package in R