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 (Development version only)

Dockstore implementation of CGP core WGS analysis

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

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.

A collection of software to work with genomic variants

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

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

🌳 Human ancestry inference from genomic data

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).

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

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

Extract and explore snv data

Genome assembly and variant benchmarks for Chinese Quartet

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