structural variant calling and genotyping with existing tools, but, smoothly.

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

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Microassembly based somatic variant caller for NGS data

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

GRIDSS: the Genomic Rearrangement IDentification Software Suite

lumpy: a general probabilistic framework for structural variant discovery

Structural variant and indel caller for mapped sequencing data

Official code repository for GATK versions 4 and up

Bayesian haplotype-based mutation calling

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository