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

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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.

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Then follow instructions in Article#1894.

Did we give you a GitHub issue to track?

For GitHub basics see Article#23405.

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Error Best Practices links for Exome Germline Variant Calling broken!

rstones12 Newcastle University UKMember ✭

February 2017 in Ask the GATK team

[email protected]

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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.

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rstones12 Newcastle University UK ✭

February 2017 Accepted Answer

cheers

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Answers

Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

February 2017

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

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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

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rstones12 Newcastle University UKMember ✭

February 2017

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

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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.

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rstones12 Newcastle University UKMember ✭

February 2017 Accepted Answer

cheers

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