Chadi Saad's starred repositories
awesome-tuis
List of projects that provide terminal user interfaces
training-collection
Collection of bioinformatics training materials
ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
VEP_plugins
Plugins for the Ensembl Variant Effect Predictor (VEP)
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
nextflow.py
Python wrapper around Nextflow.
analysis_pipeline
TOPMed analysis pipeline
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.
covid19_sequencing
As part of the COVID-19 Host Genetics Global initative, this repo serves to corroborate sample scripts for sequencing QC.
quality-control-wgs
Home for the GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations
gatk4-GenotypeGVCFs-nf
Joint calling of gVCF, following GATK4 Best Practices
GenOtoScope
Automated ACMG/AMP classification for human variants associated with congenital hearing loss
NPM-sample-qc
reference implementation of GA4GH WGS Quality Control Standards
gatk4-HaplotypeCaller-nf
GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.
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