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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

How do I obtain fastq files from a bam file?

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    Genevieve Brandt (she/her)

    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

    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

    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)

    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

    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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