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svviz

Read visualizer for structural variants

tcga_ab_compartments

A/B compartments for 12 cancer types estimated from TCGA methylation data

tensorflow

Open source software library for numerical computation using data flow graphs.

tesseract

Tesseract Open Source OCR Engine (main repository)

threads

Threads for Lua and LuaJIT. Transparent exchange of data between threads is allowed thanks to torch serialization.

titancna

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

tmad

tmux

tmux source code

tophat

Spliced read mapper for RNA-Seq

torch7

trapd

Burden testing against public controls

tsnad

Detecting somatic mutations and predicting tumor-specific neo-antigens

tumortype-wgs

Classifying tumor types based on Whole Genome Sequencing (WGS) data

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

variant_calling_pipeline

A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framework in Python.

varlociraptor

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

varscan2

Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2

vartools

Small R-package that computes CMC, KBAC and other statistical tests

vcf-to-23andme

Convert imputed DNA.Land VCF to 23andMe raw data format

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

vcfcomparator

Tool for comparing mutation calls in VCF format

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

vep_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)

verifybamid

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

verifybamid-1

viterbri-perl

Viterbi algorithm implementation in perl

vt

A tool set for short variant discovery in genetic sequence data.

wc3_maphack

A maphack for WC3 1.24d.

wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies