Note: please 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.
A snippet file is a slice of the original BAM or VCF file that 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.
-Largument 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.
If the error is happening when you're running on a VCF instead of a BAM, do the same thing but with SelectVariants instead of PrintReads.
Upload them onto our FTP server with the following credentials:
location: ftp.broadinstitute.org username: gsapubftp password: 5WvQWSfi