The current GATK version is 3.7-0
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.

#### ☞ Did you remember to?

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 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# HaplotypeCaller on 2000 samples, feasible?

United KingdomMember Posts: 404 ✭✭✭

I have previously tested HaplotypeCaller (GATK 2.7) on 100 samples. It takes a long time to run compared to UnifiedGenotyper. Is it feasible to use HaplotypeCaller on 2000 samples? Can I make it run faster other than by using multi-threading? Would it be an advantage for me to run ReduceReads prior to variant calling? I know the details are sparse, but I currently do not have any additional information. Thank you.

• United KingdomMember Posts: 404 ✭✭✭

Geraldine, thank you for your answer. I have heard from multiple sources, that HC was one of the tools used for calling SNPs for phase III of the 1000G project; i.e. 2500 samples. Would you happen to know, what procedure was used to scale to this number of samples?

It's almost like growing up hearing about the awesome dance moves of the phantom dancer "BreakArray", but nobody has ever witnessed him in action. It would be great, if you or someone else can enlighten me. Thank you.

• United KingdomMember Posts: 404 ✭✭✭

Geraldine, is your new approach for single sample variant discovery with per-site-across-samples-likelihood analysis ready? I would like to test it, if a beta is available in a developer branch.