PPT-NGS Workshop Variant Calling

Ramesh Nair 9122012 Outline Types of genetic variation Framework for variant discovery Variant calling methods and variant callers Filtering of variants Structural variants 9122012 Variant Calling. 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. Assessment. (Boston College & University of Michigan). Gabor Marth, Goncalo Abecasis, PIs. Informatics challenges for genomic analysis. Tool . building. Facilitating . analysis. . Widening. accessibility. Chris . Fields. Mayo-Illinois . Computational. . Genomics. Workshop, . June 19, 2017. Up-front acknowledgments. Many figures/slides come from:. GATK Workshop slides: . http://www.broadinstitute.org/gatk/guide/events?id=. 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. Leaving one's calling card at a friend's home was a way to express appreciation for a recent dinner party, offer condolences for an illness, or simply to say hello. If the recipient “wasn't home” a servant would accept a calling card or the card would be left in a silver tray in the entrance hall. A tray full of calling cards was like social media for the Victorian era, a way to advertise who was in one's extended social circle. Often the cards of the wealthiest or most influential people were purposefully displayed at the top of the stack to impress future visitors.. bioinformaticians. Class meetings: TR 3:30-4:50 MCGIL 2315. Office hours: M 3:00-5:00, W 4:00-5:00 CSE 4216. Contact: . mgymrek@ucsd.edu. Today’s schedule:. 3:30. -. 3:55. Sequence alignment. 4. :55-. 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. Steven Harrison. June 8 2017. sharrison@bwh.harvard.edu. RASopathies . Developmental . Delay. Cardiovascular. Metabolism. Hereditary Cancer. Sequence Variant Interpretation . WG. Harmonize recommendations for modifying ACMG guidelines. Steven Harrison (. sharrison@bwh.harvard.edu. ). March 22, 2018. SVI. Updates. Reputable source (PP5/BP6) paper. Bayes paper. PVS1 (. LOF. ) recommendation. PS2/PM6 (De novo) recommendation. Reputable Source Letter to the Editor . 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.