This workshop will introduce participants to variant calling using two methods: Genome analysis toolkit (GATK) and Deep Variant. We will develop a complete workflow for calling variants from whole-genome data for multiple individuals. The workflow will include trimming and filtering raw reads, mapping them to a reference assembly, calling variants for each individual, merging the variants of all individuals into a single variant call format file (.vcf), and filtering the resulting variant file. In addition, we will discuss strategies for reducing compute time and the comparative strengths and weaknesses of GATK and DeepVariant.
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