The current GATK version is 3.2-2

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

# Imformation in Queue output bam file

Posts: 2Member
edited January 2013

Dear all ,
I am using Queue and DataProcessingPipeline.scala ( from https://github.com/broadgsa/gatk/blob/master/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala ) 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 \ -Djava.io.tmpdir=../tmp/ \ -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
Tagged: