Loading Events

« All Events

  • This event has passed.

Genomics Series 2 — Variant Analysis

March 10 @ 1:00 pm - 4:30 pm

  1. Introduction — Basics of Variant Analysis

–Type of genetic variants

–Why study variants

–How to study variants

–Type of genetic variant studies

  1. Variant Calling

   —Workflow and pipelines

–Detection algorithms

  1. Getting ready for variant calling

–Variant ID and databases

–File format–vcf, bed, bam/sam

–How to prepare references

–Data QC and mapping

  1. Variant calling using GATK pipeline

–GATK Best practices

–Pre-processing

        • BWA, picard and GATK-format
        • Dealing with duplicates
        • Base recalibration (BQSR)

–Variant discovery

        • HaplotypeCaller
        • Germline and somatic mutation calling
        • Variant recalibration (VQSR)
        • Variant Filtering

–Preliminary analysis

        • Variant annotation/function prediction
        • Variant evaluation
  1. Variant calling using Varscan2, Samtools

–SNP/INDEL calling using Varscan2

–SNP/INDEL calling using samtools/bcftools

–Filtering and function prediction

  1. Variant Visualization

–Visualization using samtools

— Genome browser UCSC

–Standalone tool—IGV

 

Genomics Series 2 — Variant Analysis

Details

Date:
March 10
Time:
1:00 pm - 4:30 pm

Organizer

OARC
Phone:
9739721004
Email:
yc759@oarc.rutgers.edu
Website:
https://oarc.rutgers.edu/

Venue

Allison Road Classrooms (ARC) 116