This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
about the files in the bundle 2.8
as I am just starting on GATK, please could you let me know whether there is a tutorial or a description of a sequence of commands that explains how to process the NA12878 bam file in order to go through GATK pipeline and obtain the output vcf files (in ftp://ftp.broadinstitute.org/bundle/2.8/hg19/) ?
much thanks ! And also, is there a benchmark bam file for Mutect ? just to test the pipeline on ..