Day 1

GATKwr12-0-Workshop_intro

GATKwr12-1-GATK_primer

GATKwr12-2-Marking_duplicates

GATKwr12-3-IndelRealignment

GATKwr12-4-Base_recalibration

Day 2

GATKwr12-5-Variant_calling_joint_genotyping

GATKwr12-6-Variant_filtering

GATKwr12-7-Genotype_refinement

GATKwr12-8-Callset_evaluation

Day 3

GATKwr12-9-Somatic_SNPs_and_indels

GATKwr12-10-Somatic_CNVs

Computer Lab Worksheets

GATK_Discovery_Tutorial-Worksheet-AUS2016

VariantCallsetFilteringandEvaluationTutorialWorksheet-LA2016

IntroductiontoVariantCallsetEvaluationandFilteringTutorialAppendix-LA2016