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.

#### ☞ 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.

Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

Member

I don't know if this question has been asked, if so sorry.

When using UnifiedGenotyper, I was wondering if it was possible (via hidden command option, etc) to use a VCF file as a prior. Currently I have just been adding additional bam files, but it would be nice (and quicker) if I could use a Indexed file.

Shawn.

Tagged:

Hi Shawn,

What exactly do you mean by "prior"? Do you mean you have known sites, or genotypes, that you would like the UG to use in the discovery process?

• Member

Sorry about being unclear. By prior I mean known sites, i.e. 1000G.

You can provide known sites using the --dbsnp' argument, but be aware that they won't be used in any calculations; they'll just be used to populate the rsID field (if your knowns have IDs annotated).

Did you have any specific purpose in mind for using known sites, e.g. only call variants at those sites, or genotyping given alleles? There are various options to do these things, but right now I'm still not sure what you're trying to achieve so I don't know which to point you towards.

• Member

Hi Geraldine，

I would like the UG to use the posterior probability of a known site called from a sample as prior probability for calling variant of the corresponding site from another sample. Is the UG could do that?

Fuqiang

Hi Fuqiang,

No, that's not possible. You cannot influence the UG's calculation in this way.