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create PON (Panel Of Normals) from low coverage (5x) sequencing

jorgezjorgez Member
edited August 2019 in Ask the GATK team

Hello GATK team,

I would like to create a PON with CreateSomaticPanelOfNormalsto to then use it in Mutect2. Typically my tumour/normal matched pairs are Illumina PE 30X. However the available healthy samples I have for the PON are 5X, I have about one hundred of those.

Would you find sensible to build the PON from such a low coverage samples?

Many thanks
Jorge

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