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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

Read Groups - which platform (PL) to specify for Element Biosciences reads?



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    Hi Salvatore Loguercio

    Latest SAM Spec indicates the below comment

    PL  | Platform/technology used to produce the reads. Valid values: CAPILLARY, DNBSEQ (MGI/BGI),
    ELEMENT, HELICOS, ILLUMINA, IONTORRENT, LS454, ONT (Oxford Nanopore), PACBIO (Pacific Biosciences), SINGULAR, SOLID, and ULTIMA. This field should be omitted when the technology is
    not in this list (though the PM field may still be present in this case) or is unknown.

    You may use ELEMENT as PL value. This value seems to work fine with HaplotypeCaller and AddOrReplaceReadGroups tools. Others should also be fine. 


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    Salvatore Loguercio

    Awesome, thank you very much! Very useful.

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