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WGS Variant Calling: Variant calling with GATK - Part 1 | Detailed NGS Analysis Workflow
Published : 10-10-2022 - Duration : 00:48:03 - Like : 893 - Views : 44,647
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Description :
This is a detailed workflow tutorial of how to call variants (SNPs + Indels) from whole genome sequencing (WGS) data. In this video, I follow GATK best practice workflow and walk through setting up a pipeline in bash (linux) and perform steps to pre-process & align reads and ultimately get a VCF file - • Quality control (fastQC) • Alignment (BWA-MEM) • Mark Duplicate reads and BQSR • Variant calling using HaplotypeCaller In addition I also provide intuition behind performing various
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