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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

Cannot use haplotype caller on STAR-aligned data

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    Anthony Dias-Ciarla

    Hi David Condon,

    Thank you for writing to the GATK forum! I hope we can help you to sort this out.

    Firstly, you mention a User Error in the HaplotypeCaller step; I only see a BufferUnderflowException in the stack trace you included. Could you please clarify where you are seeing this error? 

    The BufferUnderflowException looks particularly unfortunate; this may be an external I/O issue. Could you also clarify whether your bam has read groups defined?

    Hopefully, the above information will help us better understand the origin of the issue. Please let me know if any other questions arise in the meantime!

    Best,
    Anthony

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    David Condon

    Hi Anthony,

    the problem is that STAR is not meant for whole-exome sequencing, so it was my fault

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