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hg19 reference fasta sequence in gatk resource bundle
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,