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Note: only do this if you have been explicitly asked to do so.
You posted a question about a problem you had with GATK tools, we answered that we think it's a bug, and we asked you to submit a detailed bug report.
The exact command line that you used when you had the problem (in a text file)
The full log output (program output in the console) from the start of the run to the end or error message (in a text file)
A snippet file is a slice of the original BAM file which contains the problematic region and is sufficient to reproduce the error. We need it in order to reproduce the problem on our end, which is the first necessary step to finding and fixing the bug. We ask you to provide this as a snippet rather than the full file so that you don't have to upload (and we don't have to process) huge giga-scale files.
Look at the error message and see if it cites a specific position where the error occurred
If not, identify what region caused the problem by running with
-L argument and progressively narrowing down the interval
-Lto write the problematic region (with 500 bp padding on either side) to a new file -- this is your snippet file.
Put all those files into a
Upload them onto our FTP server with the following credentials:
location: ftp.broadinstitute.org username: gsapubftp password: 5WvQWSfi
Post in the original discussion thread that you have done this
Be sure to tell us the name of your archive file!
Geraldine Van der Auwera, PhD