Questions people often ask
Are there any Broadspecific instructions for using GATK
Are there any public Docker images to help me build my pipeline and tools for FireCloud
Are there Best Practices for calling variants in RNAseq data
At what point should I merge read group BAM files belonging to the same sample into a single file
Can I apply the germline variant joint calling workflow to my RNAseq data
Can I get a notification when my question is answered or commented on
Can I register for FireCloud with my current nonGmail email address
Can I use different versions of the GATK at different steps of my analysis
Can I use different versions of the GATK at different steps of my analysis
Can I use GATK on nondiploid organisms
Can runtime parameter values be generated dynamically
Collected FAQs about input files for sequence read data BAMCRAM
Collected FAQs about interval lists
Collected FAQs about VCF files
Do I need to create a Google Billing Account or FireCloud Billing Project to use FireCloud
Does GATK work on nondiploid organisms
Does it matter what browser I use with FireCloud
Does my data have to live in a Google bucket to be accessible to FireCloud
FAQs about the FireCloud Free Credits Program
How can I access datasets that were cataloged in the Library
How can I attendhost a GATK workshop
How can I invoke read filters and their arguments
How can I make GATK tools run faster
How can I prepare a FASTA file to use as reference
How can I run different versions of Java on the same computer
How can I stay up to date with FireCloud features and events
How can I turn on or customize forum notifications
How can I use parallelism to make GATK tools run faster
How do I submit a detailed bug report
How do I submit a detailed bug report
How does method versioning work
How much does it cost to use FireCloud
How should I cite GATK in my own publications
How should I cite GATK in my own publications
How should I prepare for a GATK workshop
How should I preprocess data from multiplexed sequencing and multilibrary designs
How should I preprocess data from multiplexed sequencing and multilibrary designs
How should I select samples for a Panel of Normals for somatic analysis
If I publish a Workspace in the Data Library who can see it
Im new to GATK Where do I start
Lane library sample and cohort What do they mean and why are they important
Should I analyze my samples alone or together
Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data
What actions am I allowing when I register for FireCloud
What are quotas and how do I request more
What are the prerequisites for running GATK
What are the requirements for running GATK
What do I need to do before attending a workshop handson session
What do I need to set up to write and execute WDL workflows
What do the VariantEval modules do
What input files does the GATK accept require
What input files does the GATK accept require
What is a GVCF and how is it different from a regular VCF
What is a VCF and how should I interpret it
What is GATKLite and how does it relate to full GATK 2x RETIRED
What is MapReduce and why are GATK tools called walkers
What is Phone Home and how does it affect me
What is the best way to get help with FireCloud
What is the difference between QUAL and GQ annotations
What is the GATKReport file format
What is the structure of a GATK command
What is the Terra Free Credits Program
What is uBAM and why is it better than FASTQ for storing unmapped sequence data
What should I use as known variantssites for running tool X
What types of variants can GATK tools detect handle
What types of variants can GATK tools detect handle
Whats in the resource bundle and how can I get it
When should I restrict my analysis to specific intervals
When should I use L to pass in a list of intervals
Where can I find known variants training and truth sets and other resource files
Where can I find the The Cancer Genome Atlas TCGA data in FC
Where can I get a gene list in RefSeq format
Where can I get help with WDL and Cromwell
Where can I get the GATK source code
Where can I get the GATK source code Is it opensource
Which tools use pedigree information
Which training sets arguments should I use for running VQSR
Which workflow execution engines support WDL What is Cromwell
Who can publish datasets in the Library
Why are some of the annotation values different with VariantAnnotator compared to UG or HC
Why cant I create or clone a workspace