Step-by-step instructions targeted by use case

(How to) Call somatic SNVs and indels using MuTect2
(How to) Create a snippet of reads corresponding to a genomic interval
(How to) Fix a badly formatted BAM
(How to) Generate an unmapped BAM from FASTQ or aligned BAM
(How to) Map and clean up short read sequence data efficiently
(How to) Map reads to a reference with alternate contigs like GRCh38
(How to) Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
(How to) Simulate reads using a reference genome ALT contig
(howto) Apply hard filters to a call set
(howto) Call variants with HaplotypeCaller
(howto) Call variants with the UnifiedGenotyper
(howto) Discover variants with GATK - A GATK Workshop Tutorial
(howto) Evaluate a callset with CollectVariantCallingMetrics
(howto) Evaluate a callset with VariantEval
(howto) Generate a "bamout file" showing how HaplotypeCaller has remapped sequence reads
(howto) Get started with GATK4 beta
(howto) Install all software packages required to follow the GATK Best Practices.
(howto) Install software for GATK workshops
(howto) Perform local realignment around indels
(howto) Recalibrate base quality scores = run BQSR
(howto) Recalibrate variant quality scores = run VQSR
(howto) Revert a BAM file to FastQ format
(howto) Run Queue for the first time
(howto) Run a WDL script via Cromwell on a local machine (e.g. your laptop)
(howto) Run the GATK for the first time
(howto) Run the genotype refinement workflow
(howto) Test your GATK installation
(howto) Test your Queue installation
(howto) Visualize an alignment with IGV
About "Tutorials"
Appendix to (howto) Discover variants with GATK
Tutorial files provenance: ASHG15