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Education: Variant Analysis at NIH
Submitted by Vijayaraj Nagarajan; posted on Wednesday, January 10, 2018
February 27 - March 2, 2018
National Institutes of Health
9000 Rockville Pike
Bethesda, MD, USA
https://faes.org/biotech79
BACKGROUND
Next generation sequencing technologies have made genotyping a day to day research and diagnostic tool. Genotyping has come all the way from bench-to-bedside. Genetic variants are being used in personalized medicine to identify susceptibility genes, common disease variants and mutations relevant for diagnosis and therapy.
OBJECTIVES
Participants will use popular open source tools and techniques necessary for analysing variants starting from raw data quality control. Apart from the regular analysis like alignment, variant calling and annotation, this training will walk through participants in several advanced variant analysis methods and techniques.
HANDS-ON SKILLS/TOOLS TAUGHT
- NGS Basics, experimental design, data format
- Data quality control, preprocessing and alignment
- Germline variant calling
- Somatic variant calling
- Variant score recalibration and filtering
- Variant calling best practices
- Indels, structural and copy-number variation
- Cohort and population scale analysis
- Recombination, linkage, LOH, haplotype, allelic imbalance
- Variant annotation and association analysis
- Co-variation, causal variation, network analysis
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