Discussion Error Best Practices links for Exome Germline Variant Calling broken!

Title

Author

Category

search subcategories search archived

Tags

Date within of 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!

Sign In Register

GATK Showcase in Terra

Check out these fully configured workspaces to test drive the Best Practices pipelines and workshop tutorials with zero installation required!

Get email notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements on the blog, 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. When reporting a problem, 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.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Did we give you a GitHub issue to track?

For GitHub basics see Article#23405.

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

Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Error Best Practices links for Exome Germline Variant Calling broken!

rstones12 Newcastle University UKMember ✭

February 2017 in Ask the GATK team

[email protected]

0 ·

Best Answers

Geraldine_VdAuwera Cambridge, MA admin

February 2017 Accepted Answer

Ah, that's an older document that has been deprecated and replaced by a newer one, https://software.broadinstitute.org/gatk/documentation/article?id=6747. The old doc is still accessible at http://gatkforums.broadinstitute.org/gatk/discussion/2799

Thanks for reporting this, we'll update our links on the best practices page.

1 · Share on Twitter Share on Google+
rstones12 Newcastle University UK ✭

February 2017 Accepted Answer

cheers

0 · Share on Twitter Share on Google+

Answers

Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

February 2017

What link are you using? The doc pages work for me.

0 · Share on Twitter Share on Google+
rstones12 Newcastle University UKMember ✭

February 2017

Can you send me a URL link - this is broken https://software.broadinstitute.org/gatk/documentation/article?id=2799

0 · Share on Twitter Share on Google+
rstones12 Newcastle University UKMember ✭

February 2017

Error retrieving document -- It seems the requested document is not accessible through this webpage.

0 · Share on Twitter Share on Google+
Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

February 2017 Accepted Answer

Ah, that's an older document that has been deprecated and replaced by a newer one, https://software.broadinstitute.org/gatk/documentation/article?id=6747. The old doc is still accessible at http://gatkforums.broadinstitute.org/gatk/discussion/2799

Thanks for reporting this, we'll update our links on the best practices page.

1 · Share on Twitter Share on Google+
rstones12 Newcastle University UKMember ✭

February 2017 Accepted Answer

cheers

0 · Share on Twitter Share on Google+

or Register to comment.