The current GATK version is 3.8-0
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!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, 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. 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!

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
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Imformation in Queue output bam file

ugoodlfyugoodlfy Member
edited January 2013 in Ask the GATK team

Dear all ,
I am using Queue and DataProcessingPipeline.scala ( from ) to process my bam file . The input is a sample level bam file which has been processed by BWA aligned , Samtools sampe and Picard merge and duplicate removed . The output bam file (~200GB/sample ) is much larger than the input bam file (~80GB/sample ) . I want to know what information was added into the bam file ? Thanks a lot .My Queue version is Queue-2.1-10 . My script :

java \ -Xmx4g \ \ -jar ./Queue-2.1-10/Queue.jar \ -S ./DataProcessingPipeline.scala \ -i input.bam \ -R /db/human_g1k_v37.fasta \ -D /db//dbSnp_b137.vcf \ -run

Post edited by Geraldine_VdAuwera on

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    First, to clarify, this is not related to whether you use Queue or not; it has to do with the GATK tools that Queue is running on your behalf.

    As to why your BAM file is larger, I suggest you read the documentation to find out what the tools do. This will tell you what information is added to the file. If you then require additional clarifications we will be happy to provide them for you.

  • Thanks for your kindly help. I check the log files, and find out what tools I have use. I use these tools: RealignerTargetCreator , IndelRealigner , BaseRecalibrator , PrintReads . When IndelRealigner running , will it add some "Realign information" to the bam file ?image

Sign In or Register to comment.