Imformation in Queue output bam file

ugoodlfyugoodlfy Posts: 2Member
edited January 2013 in Ask the GATK team

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

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,423Administrator, GATK Developer admin

    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.

    Geraldine Van der Auwera, PhD

  • ugoodlfyugoodlfy Posts: 2Member

    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

    log
    log
    example.log
    5K
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