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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Member

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.

Sorry again and thank you very much for your availability.

Francesco

Tagged:

No, you want the bam files, but they're in the b37 directory (not hg19). They are aligned to the b37 reference (even though the name says hg19 -- that is a temporary glitch that will be corrected in the next release). If you want to work with hg19 you'll need to revert the files (using revertSam from Picard) and redo alignment. But if you have no preference (or external constraint) I recommend you work with b37-aligned files, since most of the resources we provide are made for b37 versions.

I hope this helps, good luck!

• Member

Thank you very much!