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# Imformation in Queue output bam file

Member
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:

## Answers

• 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.

• Member

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 ?

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