GATK4

The GATK4 genome analysis toolkit is a suite of tools handling a variety of tasks within the genome analysis pipeline. This suite consists of more than 100 tools and complete documentation is beyond the scope of this document. Each tool consists of different input requirements and the user is urged to see the full GATK4 documentation to learn more.

The areas of analysis covered by this tool are:

Area of Analysis	Description
Basecalling	Tools that process sequencing machine data e.g Illumina base calls, and detect sequencing level attributes e.g. adapters
Copy Number Variant Discovery	Tools that analyze read coverage to detect copy number variants
Coverage analysis	Tools that count coverage e.g. depth per allele
Diagnostics and QC	Tools that collect sequencing quality related and comparative metrics
Genotyping arrays manipulation	Tools that manipulate data generated by genotyping arrays
Intervals manipulation	Tools that process genomic intervals in various formats
Metagenomics and pathogen detection	Tools that perform metagenomic analysis e.g. microbial community composition
Methylation-specific tools	Tools that perform methylation calling, processing bisulfite sequences, methylation-aware aligned BAM
Other	Miscellaneous tools such as those that aid in data streaming
Read data manipulation	Tools that manipulate read data in SAM, BAM, or CRAM formats
Reference	Tools that analyze and manipulate FASTA format references
Short variant discovery	Tools that perform variant calling and genotyping for short variants such as SNPs, SNVs, and Indels
Structural variant discovery	Tools that detect structural variants
Variant evaluation and refinement	Tools that evaluate and refine variant calls such as with annotations not offered by the engine
Variant filtering	Tools that filter variants by annotating the Filter column
Variant manipulation	Tools that manipulate variant call format data

Parallel Capabilities: Varies by tool. See documentation.