Converting .bam to .fq and vice versa

Answered

Follow

Kountay Dwivedi

• November 10, 2020 15:56

How do I convert a .bam to .fq  and vice versa without losing any data?

That is, after conversion, I do not lose any original data or get any modified output (like change in read quality sqore). I want to run GATK best practices, and they require kind-of both bam and fq file. But, no matter how many sample data I download, they come in either bam format, or in fq format, but not both. So, I need help.

If it is possible, then what is the GATK-recommended way to do it?

 

Thank you.

0

• 

  Genevieve Brandt (she/her)

  • November 10, 2020 21:40

  Hi Kountay Dwivedi,

  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.

  0

  Comment actions Permalink
• 

  Pamela Bretscher

  • August 20, 2021 13:23

  Hi Kountay Dwivedi,

  Please see this tutorial and tool documentation on converting bam files to Fastq files: https://gatk.broadinstitute.org/hc/en-us/articles/4405443692571-SamToFastq-Picard-.

  Kind regards

  Pamela

  0

  Comment actions Permalink

Please sign in to leave a comment.