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There have wrong AP/DP output in the --vcf output for the mutect.1.1.4.jar
we specified --vcf output for using the the mutect.1.1.4.jar and the mutect.1.1.1.jar, the 1.1.1 version displayed it didn't define the vcf parameter, the 1.1.4 version had complete vcf result, but we found its the AP/DP column result is as the same as the sum of quality scores of reference/alternate alleles in tumor of metect default output. Could you tell me the reasons ? Thanks very much.
we find mutect.1.1.7 version in this forum and ready to try this version.