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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 2.9.0 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.

Using the GATK API to annotate my VCF

lindenblindenb FranceMember Posts: 54 ✭✭

I just quickly wrote a set of Tools to annotate my VCFs ( http://plindenbaum.blogspot.fr/2013/02/4-tools-i-wrote-today-to-annotate-vcf.html )

For example, one of those tools uses a BED/XML file indexed with tabix to annotate my VCF . (My code just uses the java api for tabix to get the XML at a given position)

Question: is there something in the GATK-API that would allow me to implement my code using the GATK-API: What kind of walker should I use ? What would be the benefits of using the GATK-API ? for example does using a gatk-walker will automatically make my code parallelizable ?

Pierre

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Answers

  • lindenblindenb FranceMember Posts: 54 ✭✭

    Thank you Mark & Geraldine. I think I'm going to play with a API next week. I've already got a bunch of question to ask but I'll try out a few things before asking some stupid questions.

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