Call and score variants from WGS/WES of rare disease patients.

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Generic human DNA variant annotation pipeline

Data management of large-scale whole-genome sequence variant calls using GDS files (Development version only)

Dockstore implementation of CGP core WGS analysis

This guide outlines a step-by-step process for managing your WordPress plugin to add/update in the WordPress repository using SVN (Subversion). SVN is a version control system that helps you track changes, collaborate with others, and maintain a history of your project.

🌳 Scalable ancestry from genomic data

xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.

Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

Flexible Trio DNV detection on existing VCFs.

Predictive marker discovery for groups; binary data, genomic data (single nucleotide variants), arbitrary character data.

Genome assembly and variant benchmarks for Chinese Quartet

TCGA hg19 and hg38 data downloader.

Dockstore implementation of CGP core WXS analysis

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

Extract and explore snv data

An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.

Estimates the clonal population structure in a tumour sample given a cell mutation matrix

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.

(current) Comprehensive WGS omics analysis pipeline ( reads to variants & QC ) : Sequence Platforms ( Illumina, PacBio, ONT, Ultima, Roche )

a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow

In this repository I backup the pipelines I write for the project I am involved

Assessing the performance of 28 pathogenicity prediction methods on rare single nucleotide variants in coding regions

Simulator of SNVs and CNAs in single-cell DNA sequencing

GATK WGS workflow

Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.

RAVA (Reference-based Analysis of Viral Alleles) is a Nextflow-based pipeline for non-longitudinal viral NGS data that generates interactive browser visualizations and aggregate mutation tables.

maftools for SNV mutation analysis, summarizes, and visualization