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Variant calling on Tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper?
According to your experience, what do you suggest for calling variants in tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper? Have you seen any (major or minor) difference with both the callers on same exome tumor samples? What's your advice. Do you have any reference publication(s) where HaplotypeCaller is used on tumor samples?