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Use of Population frequencies in Contamination Estimation?

VaishnaviVaishnavi United StatesMember
edited June 2014 in Ask the GATK team

Hi,

I am trying to understand the statistics and methodology behind ContEST.

However, I am not able to understand why Population Frequency is required in the first place. What is the role of HapMap_19_pop_freq.vcf file's role in contamination estimation?

Looking forward to a reply.

Thanks, Vaishnavi

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