MergeBamAlignment input files?

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Cora Olpe

• November 18, 2020 14:37

Hi, I am new to RNASeq data analysis but was hoping to use your best practices to look for somatic variants in my data. I have aligned my reads with STAR but now I'm stuck at MergeBamAlignment.

b) What does unmapped.BAM in this context mean?

Am I meant to use the -- outReadsUnmapped of STAR, convert that fastq to BAM and use that alongside my aligned.BAM? Or is it the original BAM file from the sequencer? (To me it sounds like the latter but I just want to double check...) I've tried looking in various forums but have not been able to resolve my doubts and would be grateful for help.

Kind regards

Cora

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  Genevieve Brandt (she/her)

  • November 19, 2020 20:21

  Hi Cora Olpe,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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  woodword

  • December 03, 2020 06:53

  unmapped.BAM is the output of "RevertSam" task in the RNA germline calling workflow. It has nothing to do with STAR.

  Since most of the people use fastq files as the input of RNA germline calling workflow I personally suggest you modify the workflow as follows:

  Two fastq files > STAR align > GATK AddOrReplaceReadGroups > GATK SetNmMdAndUqTags > samtools -F 0x900 > GATK MarkDuplicates and the rest of the workflow

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  Genevieve Brandt (she/her)

  • December 04, 2020 16:37

  Thanks for your contribution to the forum woodword!

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