We make various files available for public download from the GSA FTP server, such as the GATK resource bundle and presentation slides. We also maintain a public upload feature for processing bug reports from users.
There are two logins to choose from depending on whether you want to upload or download something:
location: ftp.broadinstitute.org username: gsapubftp-anonymous password: <blank>
location: ftp.broadinstitute.org username: gsapubftp password: 5WvQWSfi
If you use your browser as FTP client, make sure to include the login information in the address, otherwise you will access the general Broad Institute FTP instead of our team FTP. This should work as a direct link (for downloading only):
Is it possible to source and read bam files directly from ftp site into Unified Genotyper without downloading them first. This option works in samtools view -- but if I try the simple straightforward way in GATK (just replacing the -I inputfilename.bam with -I ftplinktobamfile.bam ) it does not work. Is there another way of doing this? This would save me a lot of diskspace if I could do this.