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!

#### ☞ 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!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks (  ) each to make a code block.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Member Posts: 2

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?

Geraldine Van der Auwera, PhD

• Member Posts: 2

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.

Geraldine Van der Auwera, PhD

• Member Posts: 5

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