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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

BQSR no output table found

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    Genevieve Brandt (she/her)

    Hi Tamrin Chowdhury, we are implementing a change in our next release that will improve error messages for this case. The issue you are seeing here is from a strange character being present in your reference or BAM (likely a é ). Check those files for one of these characters and fix it, so that you can proceed.

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    Tamrin Chowdhury

    Thank you Genevieve Brandt for your reply. 

    I think my problem occurred for the following reason

    I used the unzipped Fasta as my referece during the BWA mapping step but in the BQSR step, I was using the fasta.gz file instead of the unzipped fasta. 

    I was able to successfully complete the BQSR step once I changed my reference fasta file. So it was indeed an error with the reference. My BAM file was okay. 

    Thank you again. 

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    Genevieve Brandt (she/her)

    Great news, Tamrin Chowdhury, glad you were able to solve the problem! Thank you for posting the solution for other users.

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