Frequently Asked Questions

Assorted questions about using GATK

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 use GATK on non-diploid organisms?
Can I use different versions of the GATK at different steps of my analysis?
Collected FAQs about VCF files
Collected FAQs about input files for sequence read data (BAM/CRAM)
Collected FAQs about interval lists
How can I invoke read filters and their arguments?
How can I prepare a FASTA file to use as reference?
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 should I cite GATK in my own publications?
How should I pre-process data from multiplexed sequencing and multi-library designs?
How should I select samples for a Panel of Normals for somatic analysis?
I'm 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 are the prerequisites for running GATK?
What do GATK workshops cover?
What do I need to do before attending a workshop hands-on session?
What do the VariantEval modules do?
What input files does the GATK accept / require?
What is "Phone Home" and how does it affect me?
What is GATK-Lite and how does it relate to "full" GATK 2.x? [RETIRED]
What is Map/Reduce and why are GATK tools called "walkers"?
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 the GATKReport file format?
What is the difference between QUAL and GQ annotations?
What is the structure of a GATK command?
What is uBAM and why is it better than FASTQ for storing unmapped sequence data?
What should I use as known variants/sites for running tool X?
What types of variants can GATK tools detect / handle?
What's in the resource bundle and how can I get it?
When should I use -L to pass in a list of intervals?
Where can I get a gene list in RefSeq format?
Where can I get the GATK source code?
Which tools use pedigree information?
Which training sets / arguments should I use for running VQSR?
Why are some of the annotation values different with VariantAnnotator compared to UG or HC?