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 2.10.2 is now available at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

Member

Hi there,
I do apologise in case this question has been answered already but I couldn't find an updated thread on it.

In my previous code I had a conditional based on the number of samples to modify the percentBad` parameter in VariantRecalibrator.
Now I get an error from my scala code as if the value were not anymore a member of the class.

Checking again in the Best Practices and in the VariantRecalibrator documentation I can't find it anymore.
Could you confirm it's not used anymore? or am I doing something wrong?

cheers,
Francesco

Tagged: