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
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
lumpy: a general probabilistic framework for structural variant discovery
structural variant calling and genotyping with existing tools, but, smoothly.
The main features of brentp/smoove are: Variant Calling.
Open-source alternatives to brentp/smoove include: arq5x/lumpy-sv — lumpy: a general probabilistic framework for structural variant discovery. broadgsa/gatk — Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the… dellytools/delly — DELLY2: Structural variant discovery by integrated paired-end and split-read analysis. ekg/freebayes — Bayesian haplotype-based genetic polymorphism discovery and genotyping. google/deepvariant — DeepVariant is a deep learning genotyping tool and DNA sequence analysis pipeline used to identify single nucleotide… illumina/manta — Structural variant and indel caller for mapped sequencing data.