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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

CollectSamErrorMetrics error

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    Anthony Dias-Ciarla

    Hi Joe Georgeson,

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

    I brought this issue to our developers and received some feedback and things for you to try. The crash seems to have occurred in a part of Picard where it’s trying to get the read group ID. It could be because either the bam didn’t have it set or it was set to something Picard didn’t like. 

    You can verify whether there is a problem with your bam file by running our GATK tool ValidateSamFile. Assuming the issue is a missing read group, you may be able to repair it by using either --samtools addreplacerg or --picard AddOrReplaceReadGroups.

    I hope this helps! Please let me know if this leads you to success. If you have any other questions in the meantime, please do not hesitate to reach out.

    Best,
    Anthony

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    Joe Georgeson

    Hi Anthony Dias-Ciarla

    Thank you for the reply, after adding read groups this function works fine.

    Best,

    Joe

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    Anthony Dias-Ciarla

    Hi Joe Georgeson,

    Great! Happy to hear that. Thank you again for contributing to the GATK forum. Please do not hesitate to reach out with any other questions that pop up in the future.

    Best,

    Anthony

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