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Appropriate WGS Mutect normal_panel

ekofmanekofman Member, Broadie

Hi,

I'm running mutect1 with WGS and am trying to figure out what the appropriate attribute to use for the normal_panel is. I'm guessing it might be this 1000 genomes file ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/, but am not sure. Any advice would be appreciated! Most of the information out there seems geared towards exomes.

Thanks,

Eric

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