This page lists some common genomics tools used in bioinformatics analysis pipelines. For a more comprehensive list see the section genomic tools in my other Repo Team Teri --> link
| Name | Functionality | Phase | Notes | Maintainers |
|---|---|---|---|---|
| GATK | comprehensive set of analysis tools | all | example pipelines on Terra.bio | The Broad Institute |
| HAIL | analysis | tertiary | runs on Spark for scalability | The Broad Institute |
| IGV | visualization | tertiary | can embed in Jupyter notebooks | The Broad Institute |
| Samtools | interact with NGS files | secondary | Reading/writing/editing/indexing/viewing SAM/BAM/CRAM... formats | open source |
| Variant Transforms | transform and load vcf files into BigQuery | tertiary | can embed in Jupyter notebooks | Google (Verily) |
| VariantSpark | variant discovery | secondary | binary format | CSIRO Bioinformatics |
| GT-Scan | variant analysis | tertiary | none | CSIRO Bioinformatics |
- 📘 Get
IGV (Integrative Genomics Viewer)tool - link from The Broad 
Learning how to work with VCF (Variant Call Format) files
link- 📘 General reference 'How sequencing works' - link
- 📘 GATK tools (from The Broad Institute) to convert genomic files - link - from/to common formats (i.e. paired FASTQ to unmapped BAM, etc...)
- 📘 How to generate a BAM file - link (& image below from The Broad)
- Working with
samtools- link
