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

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Salvatore Loguercio

• February 14, 2024 16:49

Hello,

I see from the documentation that GATK requires read groups where, among other things, platform has to be specified. According to https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
The valid values for PL (Platform) are: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.

How about Element? I have samples sequenced with this new platform and is becoming more common among sequencing centers. Does the latest GATK support Element as PL?

Thanks,
SL

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  SkyWarrior

  • February 15, 2024 08:00

  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. 

  Regards. 

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  Salvatore Loguercio

  • February 15, 2024 20:15

  Awesome, thank you very much! Very useful.

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