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

Is it possible to get same SNVs in all the samples? Or is it false positives?

Dear team,
We have been analyzing caucasian samples of various origins against HG19, and we obtained various SNVs which are present in all the samples. Some of these mutations are relevant to the disease that we are studying. So we were wondering that whether it is possible to get such a result or are these false positives. These SNVs have Phred Quality score above 30. Can you tell whether data quality is bad if we get such a result. We are getting around 2000 such SNVs and our average coverage is 15X.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Jagriti,

    It is difficult to say without seeing the calls. Generally speaking, if you are looking at an entire human genome, it is expected that your samples will have many SNVs in common. If you have followed the Best Practices recommendations (including variant filtering or recalibration) then you have a good chance that your results are okay. But it is up to you to evaluate your callset.

  • jagritijagriti indiaMember

    One thing I forgot to mention is that we are analyzing whole exome sequencing data. 1% of SNVs has come out to be common in all samples. pleasae help out!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I'm sorry but I can't help you unless you have a specific problem with our tools. Analyzing and understanding your results is your job...

Sign In or Register to comment.