We've moved!
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!

hg19 reference fasta sequence in gatk resource bundle

leukogenomleukogenom Member
edited August 2012 in Ask the GATK team

Hi all,
I have recently downloaded the ucsc.hg19.fasta (version 1.5) ref fasta sequence from your ftp site. I noticed that it is about a half a GB smaller than other HG19 downloads from other sources. Also, I noticed that ucsc.hg19.fasta.fai doesn't have chromosomes 21,x,y and a few others. Is the HG19 ref (version 1.5 or version 1.2) on your ftp complete? Please confirm so I can guide my troubleshooting.
Thanks so much,

Best Answer


  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    Hi there,

    I think you must be mistaken (or something went wrong during your download). The reference and fai files are complete on our end.

Sign In or Register to comment.