Counld I use bam files from HISAT2 to call snp/indels?

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Qun

• November 20, 2020 07:56

HI,

I have a question when I analysis Whole-exome sequencing data. I mapping data with BWA as pipeline described. However, it spend long time to mapping with BWA.  

So, counld I use bam files from HISAT2 as input to call snp/indels with GATK 4.1.9  version?

 

Sorry if I miss something important, I am pretty new in using GATK.

Thanks in advance for your time.

Qun

 

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• Official comment

  

  Genevieve Brandt (she/her)

  • July 28, 2021 01:36

  Hi Qun,

  Yes, as long as the output from HISAT2 are valid BAM files. Our best practices recommendation uses BWA, but you should be able to use HISAT2 if you prefer it. If you run into issues when you try to use these BAM files, let us know and we can help troubleshoot.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • November 24, 2020 16:50
  • Edited

  Hi Qun,

  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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