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GATK best practices Short somatic variant calling: ExAC file


I was wondering if you could give some insight in the creation/preparation of the ExAC vcf file mentioned in the jason file (mutect2.exome.inputs.json) on Github (https://github.com/gatk-workflows/gatk4-somatic-snvs-indels).

I would like to apply the GATK best practices to my own datasets, however due to subsequent steps I'll be working with hg38 instead of hg19. So in order to apply the best practices I need to adapt the different input files to hg38.

Kind regards,

Best Answer


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