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Best practices for ContEst for WGS

ekofmanekofman Member, Broadie


What are the best practices for ContEst as far as the population file and interval list parameters go? I would imagine that interval list should be irrelevant when looking across the whole genome, but this seems to be a required argument.

I'm currently using /xchip/cga/reference/hg19/hg19_population_stratified_af_hapmap_3.3.vcf‎ for the population file -- is that appropriate for WGS?

Thanks for the advice,



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