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

Errors about read group (RG) information Follow


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    Stephen Johnson

    Thank you for this example of how to use AddOrReplaceReadGroups! Would a specified RGPU also be a required for this to run?

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    Marlene Jara

    Thank you, while running it also asked for the RGPU  as mandatory input.

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    Alexsandre Gutiérrez Barragán

    Thank you. I sequenced in a MGI platform, so MGI is not a valid value for -RGPL when using AddOrReplaceReadGroups, what can I do to avoid this ERROR in HaplotypeCaller?

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