Oy vey, veering off topic, but whatever... BAM is a sequence of zlib-compressed blocks. Each of them has a checksum, and any corruption gets past it with prob

Oy vey, veering off topic, but whatever... BAM is a sequence of zlib-compressed blocks. Each of them has a checksum, and any corruption gets past it with probability 2^-32. Any sane software will give you an error. When in doubt, just decompress the stupid file using gunzip or zcat, those will verify the checksum. Don't guess, check. But if you insist on using software that just ignores the checksum (I think, not even samtools, which segfaults(!) on misspelled file names(!) is that awful), all bets are off. Decompressing a corrupted file yields nonsense that doesn't even have the same length as the original data. BAM would also quickly get out of sync, and subsequent records would contain complete nonsense. You'd know if you saw that. However... > you are positive that BAM files should be self consistent? That is a loaded question. In addition to being syntactically correct, BAM files should maintain a few variants that are hard to check. They rearely do. BWA(!) produces inconsistent BAM files, and I've seen many, many scripts in the wild that produce complete bullshit that only happens to work in a very specific setting. Like I said, you're probably using some awful software.