Genome Analysis Toolkit

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

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    Genevieve Brandt

    Hello, for posts regarding GATK issues, we require three items to be included in the post.

    1. GATK version number
    2. Exact command used
    3. Complete Stack Trace/Error log [Use -DSTACK_TRACE_ON_USEREXCEPTION to print the stack trace.] How to submit java arguments.

    Your post is missing one of these items that must be included so that we can thoroughly look into the problem.

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    Rayz Ghimire

    Hi Genevieve Brandt sorry about that. 

    1. GATK version number -  gatk-4.8.1
    2. Exact command used /path/to/gatk ApplyBQSR -R assembly38.fasta -I test12.dedup.bam --bsqr-recal-file sample12_recal_data.table -O sample12.recal.bam
    3. Complete Stack Trace/Error log [Use -DSTACK_TRACE_ON_USEREXCEPTION to print the stack trace.] : A USER ERROR has occurred: Couldn't read file. Error was: sample12_recal_data.table with exception : sample12_recal_data.table (No such file or directory). 

    I checked numerous times but this file is there. 

    Thank you 

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    Genevieve Brandt

    A couple questions:

    • What are the file permissions for the sample12_recal_data.table file?
    • Check if the table is in the correct format, and that it is not corrupted
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