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adamajava

annotsv

Annotation and Ranking of Structural Variation

babaomo

This is a group of code libraries and tests for determining the combined paternity index in paternity tests.

bamclipper

Remove primer sequence from BAM alignments by soft-clipping

bamql

Query language for filtering SAM/BAM reads

bioinfortools

Bioinformatics scripts and tools

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

cancervar

Clinical interpretation of somatic mutations in cancer

classifycnv

ClassifyCNV: a tool for clinical annotation of copy-number variants

cnv-sim

Copy Number Variations (CNV) Simulator

cnvbenchmarker

Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data

cnvscan

detect somatic copy number from capture NGS data

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dl4vc

exomedepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

exomedepth_pipeline

Our approach for calling CNVs on NGS using ExomeDepth

expansionhunterdenovo

A suite of tools for detecting expansions of short tandem repeats

fgbio

Tools for working with genomic and high throughput sequencing data.

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

gatk

Official code repository for GATK versions 4 and up

genomomff

giab_tools_methods

This repository contains a list of tools or methods that have been used in GIAB analysis

gittest

hap.py

Haplotype VCF comparison tools

hbos-cnv

HBOS-CNV: a new approach to detect copy number variations from next-generation sequencing data

hla

xHLA: Fast and accurate HLA typing from short read sequence data

i-s00n

intervar

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

jvarkit

Java utilities for Bioinformatics

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.