PPT-NGS Workshop Variant Calling and Structural Variants from

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Exomes WGS Ramesh Nair May 31 2013 Outline Types of genetic variation Framework for variant discovery Variant calling methods and variant callers Filtering of variants

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NGS Workshop Variant Calling and Structural Variants from: Transcript

Exomes WGS Ramesh Nair May 31 2013 Outline Types of genetic variation Framework for variant discovery Variant calling methods and variant callers Filtering of variants Structural variants. Presented by Derek Bickhart. Presentation Outline. Variant classification and detection. Theory on read structure and bias. Simulations and real data. Genetic . Variation. Single nucleotide variations – SNP (human . Credits for slides: Dan . Newburger. What is Cancer?. Definitions. A class of diseases characterized by malignant growth of a group of cells. Growth is uncontrolled. Invasive and Damaging. Often able to metastasize. Deanna M. Church . Staff Scientist, NCBI. @. deannachurch. Short Course in Medical Genetics 2013. FASTQ. BAM. VCF. VCF. FASTQ. BAM. VCF. VCF. Steve Sherry, NCBI. http://. www.bioplanet.com. /. gcat. http://. Variant Calling. Ramesh Nair. 9/12/2012. Outline. Types of genetic variation. Framework for variant discovery. Variant calling methods and variant callers. Filtering of variants. Structural variants. Variant Calling and Structural Variants from . Exomes. /WGS. Ramesh Nair. May 30, 2014. Outline. Types of genetic variation. Framework for variant discovery. Variant calling methods and variant callers. NGS/. MPS. Precourse. . materials. Yonglan Zheng. (yzheng3@uchicago.edu). 2017.6.10. Precourse. . materials. General NGS variant calling workflow . [slide#3. ]. GATK . Best Practice as an . example. ZOOM ON. . GATK. Cedric Notredame. Adapted from . Yannick. . Boursin. Genetic. . variations. Variations . at the (A) . nucleotide level. . and. (B) . structural level. (C) Single nucleotide . polymorphism . Karchin Lab. Department of Biomedical Engineering. Institute of Computational Medicine. Johns Hopkins University. SSID: . ASHGWORKSHOP. WiFi. Password. : . ASHGWORKSHOP. Select the SSID: . ASHGWORKSHOP. Professor . Department of . Epidemiology and. Genetic Epidemiology Research Institute. University . of . California, Irvine. . Irvine, CA. kedward1@uci.edu. What is old is new. Rare Variants. This session. Tutorial. ICHG 2011. Montreal. , Quebec, Canada. October 13, 2011. Intro. International project to construct a foundational data set for human genetics. Discover virtually. all common human variations by investigating many genomes at the base pair level. Introduction. This slide presentation covers several topics pertaining to Variant classification, reclassification and the . V. ariant . C. lassification . P. rogram (VCP). You may view the presentation in its entirety or click on one of the topics below to go directly to the relevant slides.. Presented by Derek Bickhart. Presentation Outline. Variant classification and detection. Theory on read structure and bias. Simulations and real data. Genetic . Variation. Single nucleotide variations – SNP (human . Ramesh Nair. 9/12/2012. Outline. Types of genetic variation. Framework for variant discovery. Variant calling methods and variant callers. Filtering of variants. Structural variants. 9/12/2012. Variant Calling. and . Jen . McGlaughon, Ph.D. .. Biocurator. Working Group. 10/26/17. Case-Control Studies. Case cohort. Individuals ascertained from an institute, academic medical center, etc. or from multiple centers based on a given phenotype or disease..

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