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

GATK mark duplicates error



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    Kshama Aswath

    So adding to the above post:

    even if it is a "harmless" error and I can ignore it,  could it be a memory issue? I ran it default and did not specify any memory allotment. If that is the case, is there a guide on memory needed ( roughly) on different tools. I understand input file sizes varies and it is hard to say exactly how much to allot, but a ball park idea could hlep. Thankyou !

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    Genevieve Brandt (she/her)

    Hi Kshama Aswath, please post the entire error message so we can look into the problem. 

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