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Ion PGM and GATK

hwills89hwills89 EdinburghMember

After recently attending a GATK best practice workshop it was mentioned use of GATK with data produced from the IonPGM was not advised. Could you please elaborate on the reasons why? And also point me in the direction of an alternative variant caller for somatic mutations for cancer samples which may be suitable for making calls for clinical utility.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @hwills89,

    Thanks for attending our workshop! The technology used by Ion has an error mode (producing spurious indels) which GATK cannot properly compensate for, so we recommend following Ion's recommendations (which I believe include using their specialized variant caller). I don't know what is their caller's performance for somatic variant calling; this is not something we have experience with.

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