As you recommended doing sensitivity and PPV evaluation using truth data in the seminar, what truth data do you recommend using for that purpose??

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Yuting He

• November 17, 2020 15:56

a)How do I (......)?

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  Mark Fleharty

  • November 17, 2020 16:01

  We typically used pooled Hapmap samples.  We pool them in equal fractions of 5, 10 and 20 samples.  This gives us a distribution of truth variants as low as 2.5% allele fraction.

   

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  Mark Fleharty

  • November 17, 2020 16:17

  I would also encourage you to take a look at:

  https://www.biorxiv.org/content/10.1101/825042v1.full

  This describes. LinSeq, which is one of the ways we use to construct somatic truth data.

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