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VariantEval for whole exome data

yl01yl01 Member Posts: 0
edited January 2013 in Ask the GATK team

Hello,

I found the materials of the BroadE Workshop very helpful, especially the slide on analyzing variant calls using VariantEval, because there is not much documentation for it on GATK site. As an example 62 whole genome sequencing samples from north Europe were evaluated together with 1000G FIN samples, and also the polymorphic and monomorphic sites on the 1000G genotype chip were used as comparator. I would like very much to do the same for our whole exome data, the question is: is there good quality whole exome data that I can use to evaluate our own exome data?

I have checked the NHLBI ESP project Exome Variant Server site, the vcf files can be downloaded doesn't have the genotype data.

Thanks in advance!

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,421 admin

    Hi there,

    That's not something we can answer, as it depends on your data and experimental design. But hopefully other users in the community may chime in and share their experience and resources. Good luck!

    Geraldine Van der Auwera, PhD

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