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!

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.
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.

#### ☞ 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.

GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

# Variant Recalibration - Number of Whole Exome Samples Needed and Where?

Member
edited October 2012

Hello,

I've just made a long needed update to the most recent version of GATK. I had been toying with the variant quality score recalibrator before but now that I have a great deal more exomes at my disposal I'd like to fully implement it in a meaningful way.

The phrase I'm confused about is "In our testing we've found that in order to achieve the best exome results one needs to use an exome callset with at least 30 samples." How exactly do I arrange these 30+ exomes?

Is there any difference or reason to choose one of the following two workflows over the other?

1. Input 30+ exomes in the "-I" argument of either the UnifiedGenotyper or HaplotypeCaller and then with my multi-sample VCF perform the variant recalibration procedure and then split the individual call sets out of the multi-sample vcf with SelectVariants?

2. Take 30+ individual vcf files, merge them together, and then perform variant recalibration on the merged vcf and then split the individual call sets out of the multi-sample vcf with SelectVariants?

3. Or some third option I'm missing

Any help is appreciated.

Thanks

Post edited by Geraldine_VdAuwera on
Tagged: