How do I obtain fastq files from a bam file?

Answered

November 02, 2020 15:28

Hello,

I would like to convert a bam file (thas has been generated following GATK Best Practices - Data pre-processing for variant discovery) to initial fastq files (R1 and R2).

I thought I could use SamToFastq Picard's tool.

I did not find any pipeline with "SamToFastq" in the Best Practices. So I just wanted to be sure that I can use SamToFastq and only that (in other words, that no additional step is needed to retrieve fastq files able to enter a new pre-processing pipeline).

Thanks in advance for you help!

5 comments

Genevieve Brandt (she/her)

November 05, 2020 23:48
Maguelonne please see the tool documentation page for SamToFastq: SamToFastq (Picard). The input is a BAM or SAM and the output is a FASTQ.
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Kountay Dwivedi

November 11, 2020 04:35
Hi,

I am also having an issue regarding conversion of .fq to .sam/.bam

In the GATK Best Practices, in order to execute the step MergeBamAlignment, we need a uBam file and aligned bam file. However, the sample that I have in hand is in .fq format, which is the requirement of bwa mem tool for alignment.

How do I get the desired uBam file?

Thanks
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Kountay Dwivedi

November 11, 2020 04:45
Hi Maguelonne ,

Would it be possible for you share the details of sample dataset that you're using, if any?
I am unable to find proper sample data over which I could practice GATK Best Practices.

Thanks
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Genevieve Brandt (she/her)

November 17, 2020 16:54
Hi Kountay Dwivedi, you may find these tutorials at our platform Terra to be helpful to better understand GATK. There are example commands as well as locations of tutorial data there.

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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Pamela Bretscher

August 20, 2021 13:18
Hi Kountay Dwivedi,

Please see the following tutorial on generating a uBAM file from a Fastq file: https://gatk.broadinstitute.org/hc/en-us/articles/4403687183515--How-to-Generate-an-unmapped-BAM-from-FASTQ-or-aligned-BAM

Kind regards,

Pamela
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