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MuTect in High Confidence (HC) mode
In the MuTect Nat Biotech paper the authors discuss the STD, HC and HC+PON filtering modes, however in the online manual (http://www.broadinstitute.org/cancer/cga/mutect_run) there is no indication of how to use the 3 modes, I was wondering if it was possible to clarify this point. Now I am using the following command:
java -jar muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ref.fa --cosmic cosmic.vcf --dbsnp dbsnp.vcf--input_file:normal normal.bam --input_file:tumor tumor.bam --out tumor.mutect