The current GATK version is 3.7-0
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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.

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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

I want to know if GATK can do what I want! NGS reads, polyploids, phylogeny

joqbjoqb Member
edited January 2013 in Ask the GATK team

Hello,
I have 454 reads of loci on polyploid individuals. I am able to produce assemblies containing the different copies of one locus per individual. But I want to extract the reads corresponding to each copies, to then be able to produce phylogenies.
Does the GATK can do something like this?

Thanks,

Answers

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