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Use vcf from HaplotypeCaller as normal_panel with Mutect2 (GAKT4.beta.6) ?
I am trying to find somatic mutations in blood samples. The same samples were used previously to detect germline variants with HaplotypeCaller. Does it make sense to use the vcf obtained for a given sample from HaplotypeCaller as a --normal_panel parameter with Mutect2 in order to detect only somatic variants in that sample ? Or should I use another parameter to pass the germline variant list on ?
Many thanks for your answer,