Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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