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!

Did you remember to?


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.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
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.

Data Processing Pipeline

mike_boursnellmike_boursnell Member Posts: 94
edited August 2012 in Ask the GATK team

Can the DataProcessingPipeline (as used by Queue.jar) be used to process BAM files in the best recommended way ("Best: multi-sample realignment with known sites and recalibration")

Best Answer

Answers

  • CarneiroCarneiro Charlestown, MAMember Posts: 274 admin
    edited August 2012

    Although the Data Processing Pipeline follows our best practices guidelines, it is provided as an example script for people to build their own. You risk using parameters that are not updated or best for your particular data set.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    What my esteemed colleague @Carneiro means to say, I believe, is that the DPP script performs the necessary steps described in the Best Practices, but you should not simply run it with default parameters. You should check that the way the steps are set up make sense for your dataset and above all make sure you adapt the parameters to the specificities of your data.

    Geraldine Van der Auwera, PhD

  • mike_boursnellmike_boursnell Member Posts: 94

    Thanks for the folloe up. :-) What I was trying to ask is this: The "Best" recommended processing of BAM files seem to involve processing multiple BAM files together (i.e. in parallel rather than in series). Can the DPP do this, and if so how do I set it up to do that?

  • CarneiroCarneiro Charlestown, MAMember Posts: 274 admin
    Accepted Answer

    No, the DPP as is will split all bam files per sample and process them independently. Just to reiterate, the DPP script is an example script. You are welcome to modify it to do all samples at once, using the DPP as a template.

Sign In or Register to comment.