zihhuafang

production-pipelines

Genomics workflows for CPG using Hail Batch

needLR

A structural variant filtering and prioritization tool for long-read sequencing data

SV-MeCa

SV-MeCa integrates leading standalone SV callers into an automated workflow, leveraging VCF-retrieved quality metrics. Using an XGBoost classifier, SV-MeCa ranks SV calls by evidence to represent true positive events

Gene-Burden-Analysis

deeprvat

TRIBES

Finding cryptic relationships to boost disease gene detection

ASMC

Ascertained Sequentially Markovian Coalescent

CoCoRV_nextflow_singularity

Implementation of CoCoRV pipeline using Nextflow and Singularity

mitoCN

Estimate mitochondrial DNA copy number from whole genome sequencing data

STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

FAVORannotator

SV-ADSP-Pipeline

For ADSP 17k SV analysis

structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

amp-pd-workflows

Pipeline definitions used to construct AMP-PD data products

analysis-wdls

Scalable genomic analysis pipelines, written in WDL

analysis_pipeline

TOPMed analysis pipeline

gnomad-mitochondria

GLnext

Scalable gVCF merging and joint variant calling

REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

ExpansionHunter

A tool for estimating repeat sizes

rvnpl

STRchive

Short Tandem Repeat disease loci resource

AGAIN

Genome-wide detection of AG-gain variants between the splicing branchpoint and canonical acceptor site in human introns

DeNovoCNN

A deep learning approach to de novo variant calling in next generation sequencing data

saige-pipelines

CHARR

Contamination from Homozygous Alternate Reference Reads

SCE-VCF

Sample Contamination Estimate from VCF

MutScore

ClinCNV

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

nitrogenase

Workflows for interation of Knowledge Portals and BioData Catalyst