chadisaad

fingerprint_maps

Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.

analysis_pipeline

TOPMed analysis pipeline

quality-control-wgs

Home for the GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations

universal-saige

DiNAMO

Discriminative DNA IUPAC motif discovery tool

nextflow.py

Python wrapper around Nextflow.

nextflow-api

GenOtoScope

Automated ACMG/AMP classification for human variants associated with congenital hearing loss

tapes

TAPES : a Tool for Assessment and Prioritisation in Exome Studies

awesome-tuis

List of projects that provide terminal user interfaces

crg2

Research pipeline for exploring clinically relevant genomic variants

VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

vcf-split

Split combined-sample VCF stream into single-sample VCF files

training-collection

Collection of bioinformatics training materials

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline

wgs-sample-qc

visit https://github.com/ga4gh/quality-control-wgs instead. Repository to host ongoing discussions by GHIF members on developing a reference implementation for QC of WGS results

NPM-sample-qc

reference implementation of GA4GH WGS Quality Control Standards

DRAGMAP

DRAGEN open-source mapper

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Pipeline-Standardization

warp

WDL Analysis Research Pipelines

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

WES.WGS

Covid-19 HGI WES/WGS burden test BQC-19 pipeline

hail

Cloud-native genomic dataframes and batch computing

regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

gatk4-GenotypeGVCFs-nf

Joint calling of gVCF, following GATK4 Best Practices

gatk4-HaplotypeCaller-nf

GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.

covid19_sequencing

As part of the COVID-19 Host Genetics Global initative, this repo serves to corroborate sample scripts for sequencing QC.