Dear all, I am really a newbie in NGS, so I apologize if I say something completely wrong. In order to start to manage this kind of data I am trying to follow the workflow described in http://www.broadinstitute.org/gatk/guide/topic?name=intro. It'suggested to download the "raw and realigned, recalibrated NA12878 test data from the GATK resource bundle". When i connect to the ftp through Filezilla I cannot find the bam file of NA12878 (/bundle/hg19) but only the vcf files. Is it correct? Should I download the vcf files?
Sorry again and thank you very much for your availability.