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SUMMARY:HPC in life science—Genomics Series2\, Variant analysis on Amarel cluster
DESCRIPTION:Please register to attend this workshop at the bottom of this page. After filling out the registration form\, we will email you the Zoom link. \nAmarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible. \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nIf you have questions or need help\, please contact Janet Chang. \n1. Introduction – The Basics of Variant Analysis \n\nConcepts of genetic variant\nThe journey of variant study\nSignificance\nChallenges\n\n2. Variant Analysis –Overview \n\nWorkflow and informatics tools\nVariant detection methods\nVariant calling algorithms\nVariant annotation and functional prediction\nVariant prioritization\, filtering\, and validation\n\n3. Variant Analysis – Getting ready \n\nFile format—fastq\, vcf\, bed\, bam/sam\nVariant ID and databases\nVariant Reporting\nVariant visualization\n** Variant analysis of COVID-19 genomes\n\n4. Variant calling pipeline example — GATK \n\nGATK Best practices\nPre-processing\n\nBWA\, picard and GATK-format\, Dealing with duplicates\,\nBase recalibration (BQSR)\n\n\nVariant discovery\n\nHaplotypeCaller\, Germline and somatic mutation calling\,\nVariant recalibration (VQSR)\, Variant Filtering\n\n\nPreliminary analysis\n\nVariant annotation/function prediction\nVariant evaluation\n\n\n\n5. Variant calling pipeline example — Varscan2\, Samtools \n\nSNP/INDEL calling using Varscan2\nSNP/INDEL calling using samtools/bcftools\nFiltering and function prediction\n\n6. Labs \n\nLab1 — Pre-processing\, QC\, mapping\, and reference preparation\nLab2 — GATK pipeline\nLab3 — Samtools and varscan2 pipelines\nLab4 — Variant annotation/ Functional prediction\nLab5 — Visualization\nLab6 — Manage your jobs using slurm job scheduler\n\n \n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/hpc-life-science-genomics-series2-10-8-21/
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