The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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