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

Error while running HaplotypeCaller


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    James Emery

    Hello Achint Kumar, Can you check that you have a valid bam header for Data/Outputs/output_wgs.bam? That error could be generated if there is an issue extracting the SM tag from the RG IDs for from the bam header. I would like to diagnose what is causing this stack-trace since you shouldn't be seeing that at all. You can run `$ samtools view -H __.bam` to view the header and you should see a bunch of @rg fields with the SM:<SAMPLENAME>. How was your bam generated and can you make sure that its generating a valid bam header? 

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