(howto) Retrieve the time and cost of a completed workflow
1 howto Write your first WDL script running GATK HaplotypeCaller
2 howto Write a simple multistep workflow
3 howto Run a sample variant discovery minipipeline
4 howto Use scattergather to joint call genotypes
Appendix to howto Discover variants with GATK
Guidelines for working with Docker Images and Dockerfiles Broadies only
How to Call somatic mutations using GATK4 Mutect2
How to Call somatic SNVs and indels using MuTect2
How to Consolidate GVCFs for joint calling with GenotypeGVCFs
How to Create a snippet of reads corresponding to a genomic interval
How to Execute Workflows from the gatkworkflows Git Organization
How to Filter on genotype using VariantFiltration
How to Filter variants either with VQSR or by hardfiltering
How to Fix a badly formatted BAM
How to Generate an unmapped BAM from FASTQ or aligned BAM
How to Install and use Conda for GATK4
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 Access TCGA Controlled Access Data Workspaces
howto Add users to a FireCloud Billing Project
howto Apply hard filters to a call set
howto Call variants with HaplotypeCaller
howto Call variants with the UnifiedGenotyper
howto Cite FireCloud Cromwell or WDL in your publications
howto Configure a method in a workspace
howto Create a new FireCloud Billing Project
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 Generate a JSON file describing inputs
howto Get started with GATK4 beta
howto Install all software packages required to follow the GATK Best Practices
howto Install Docker and test that it works
howto Install software for GATK workshops
howto Install software for WDL workshops
howto Make a docker image the easy way using a base image
howto Overwrite and delete data from the data model
howto Perform local realignment around indels
howto Prepare for a FireCloud 101 workshop
howto Publish a docker container image to Google Container Registry GCR
howto Recalibrate base quality scores run BQSR
howto Recalibrate variant quality scores run VQSR
howto Register get an account to use FireCloud
howto Revert a BAM file to FastQ format
howto Run a WDL script via Cromwell on a local machine eg your laptop
howto Run Queue for the first time
howto Run the GATK for the first time
howto Run the genotype refinement workflow
howto Set up a Google Billing Account Broadies only
howto Set up a Google Billing Account nonBroad users
howto Set up an environment to test your workflows locally
howto Set up use and shut down a Notebook
howto Test your GATK installation
howto Test your Queue installation
howto Upload files to your Google bucket
howto Use my own tools in FireCloud
howto Validate your WDL script syntax before execution