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Illumina Pipeline

Hello everyone, I'm currently working with an Illumina pipeline where we do the following:

1. Align reads against reference genome using Isaac
2. Call structural variants using Manta
3. Call small germline variants (SNVs and indels) using Starling
4. Call copy number variants (CNVs) using Canvas (use of a WT DNA as control)
5. Annotate variants with Illumina Annotation Engine
6. Calculate alignment and variant calling metrics using Pluggable Universal Metrics Analyzer (PUMA)

Do you know if (and how) this can be done with GATK4? Would you tell me, please, the tools that I should use?
Are there any alternative open-source tools that can also be 'explored'?

Thank you in advance,

Henry L.


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