Session: Genomics, Bioinformatics, and Variant Calling

Division: Workshops

Title: Genomics, Bioinformatics, and Variant Calling

Lead Community Sponsor:
Cosponsor: ASA Section: Biometry and Statistical Computing
Community Cosponsor: Bioinformatics in Crops and Soils Community
Format: Oral None (Admin Only)
Keywords:

Session Description: Next generation sequencing has revolutionized the field of human and agricultural sciences. Major crop species have their genomes sequenced in the last decade. The drop in genome sequencing cost and the availability of robust analytical tools may soon break the barriers to deliver $100 genomes. Additionally, this may further enable progress in the areas of pan-genomics, metagenomics, single-cell genomics, and the discovery of genetic variation across populations. These topics have a direct impact on the members of the tri-societies. Hence, this proposed workshop will cover the following topics: (1) Genomics, sequencing, and their implications in agriculture; (2) UNIX shell scripting and regular expressions; (3) Variant calling overview, file formats, inspection of sequence data quality, and indexing genome assembly; (4) Variant calling; (5) Quality control of variants; and (6) Annotation of variants. The workshop assumes an understanding of introductory genetics, some familiarity with the UNIX command-line, and does not need any scripting experience. The workshop will be interactive and involve hands-on exercises on genomics data analysis and interpretation. At the end of this workshop, the attendees will be able to run jobs on a high-performance computing cluster, use and apply command-line skills, perform variant calling using short read sequence data and a reference genome, and generate variant (SNPs/Indels) calls for downstream applications such as bi-parental mapping, genome-wide association studies, and genomic selection.