The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Genotyping strategy for using UnifiedGenotyper

skblazerskblazer Member
edited December 2012 in Ask the GATK team

Dear GATK authors,

I have two little questions about the genotyping strategy for using UnifiedGenotyper.

1) Imaging I have a list of candidate sites in hand, then I just want to use UG to genotype my individuals at these sites. Considering the sequencing coverage for each individual is low or median, will there be any difference between genotyping them on individual level and on a cohort of population level?

2) I have a list of candidate sites, including SNPs and complex indels, which were discovered by HaplotypeCaller, Then can I use UG to genotype these sites across individuals to get the correct genotypes? I know HC used a local denovo assembly to discover the variants, but I'm not sure after the variants have been discovered, whether there is any difference in genotyping result between HC and UG.


Best Answer


Sign In or Register to comment.