gatk_variantcalling_tutorials.md

Tutorials

• Variant Calling Pipeline using GATK4
• GATK4 Best Practice Nextflow Pipeline
• Variant calling in human whole genome/exome sequencing data
• Germline short variant discovery (SNPs + Indels)
• W8: Variant Calling with GATK - Day 1
• W8: Variant Calling with GATK - Day 2

Datasets

• Does GATK provide datasets to test their pipelines? (Learning purpose)
• 2019 Simple SNP calling pipeline in Linux