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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

Problems with FastQtoSAM



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    Bhanu Gandham

    Siddharth Prakash

    Can you please provide the following:

    1. Can you please share the entire stack trace for this? You can print the stack by using this java option (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true')
    2. Please run the command with the stack-trace on one of the failed samples and share the exact command used for it and the entire stack trace
    3. Also please share a few lines from the fastqs that is ending in the error and a few lines from the fastqs that run successfully without an error. Maybe the first 8 lines from fq1 and fq2
    4. Please also share the exact command and the entire stack trace for one of the samples that worked without any error.
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    Charlie Jacob

    I have also this problem please share some solution Thanks Charlie Jacob

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    Genevieve Brandt (she/her)

    Hi Charlie Jacob, if Siddharth Prakash does not respond with more information, go ahead and provide more information regarding your issue so we can look into it further. Here are our recommendations for a post:

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