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 https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

# Calibration of QUAL field emitted by the Unified Genotyper

Member, Broadie

Hi,

I am looking at the distribution of quality scores (QUAL column of VCF) emitted by the Unified Genotyper v1.4 (old version, sorry ) for SNPs called on 769 samples with 12x coverage HiSeq data. The median quality score is at ~Q750 and the mean at ~Q28000. I was just wondering if you could comment on how well calibrated these quality scores are and whether/how the number of samples and/or coverage would affect them?

Thanks in advance,
Laurent

Tagged:

## Answers

• Cambridge, MAMember, Administrator, Broadie

Hi Laurent,

I'm not quite sure what you mean by calibration for the variant quals? The QUAL will indeed depend on coverage and number of samples, since both can increase or decrease confidence in a given call according to the calling model. Basically it is a question of how many observations are available from which to make a call. If you want to known exactly what is the mathematical relationship you'll need to look at the code of the model calculations for the version that you are using.

• Member, Broadie

Hi Geraldine,

Thanks for your answer. What I mean is that QUAL is expressed as a phred score (if I'm not mistaking) and so Q28000 is a rather astronomical number then. I'm just trying to get a sense of how to interpret these values and whether I should really look at them in a relative way (i.e. in the same calling experiment, a site with higher quality has a higher posterior) or if they can be interpreted in an absolute way too.

Thanks,
Laurent

• Member, Broadie

Thanks Geraldine,

This was helpful in clarifying my issue!

Cheers,
Laurent

Sign In or Register to comment.