Probably you already checked your file and moved on, but I want to come back to this issue because I have read in more depth the samtools quickcheck manual and I have an objection.
Here you have what the manual says about how it works:
"""Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM only).
Data in the middle of the file is not read since that would be much more time consuming, so please note that this command will not detect internal corruption, but is useful for testing that files are not truncated before performing more intensive tasks on them.""""
For example, I have a BAM file that gives no error with samtools quickcheck, but when I see it with samtools flagstat it tells me it's empty (no reads, no nothing, when it's supposed to have the information of 32939748 reads). This is an example of a case where samtools quickcheck can mislead you into thinking there's no problem with your BAM/SAM when there's actually one (you could eventually test it yourself to see what I mean). Probably it's because the BAM still has the parts that samtools quickcheck checks, therefore giving a positive result there.
With all that being said, I recommend Picard Tools's "ValidateSamFile" (works for BAM as well, helped me with my problem). https://software.broadinstitute.org/gatk/documentation/article.php?id=7571. I think it's more comprehensive than the other methods, since it was designed to tackle down this particular issue. In the old syntax this is (check the manual for the new, but this is what I used):
java -jar /path/to/picard.jar ValidateSamFile I= myfile.bam MODE=SUMMARY
Coming back to the example of my problem, ValidateSamFile told me there was a problem: ERROR:MISSING_READ_GROUP. I converted my BAM to SAM and this was the content:
@HD VN:1.3 SO:coordinate
In my script, where this file was generated, the reads were mapped, the sam was produced correctly but there was a mistake in the convertion to BAM. When I checked the BAM with quickcheck, it had the beginning and end-of-file, therefore it gave an answer as if the file was ok, which is wrong. Now, thanks to ValidateSamFile and samtools flagstat I know my script has a problem, but if I had only checked with quickcheck I would think the files are great and I would have continued with my pipeline without further questioning, until hitting myself with the wall, eventually.
I also ran samtools quickcheck on this new sam file and also did not output anything (told me everything was ok). So far, then, samtools flagstat helped me visualize that there were no reads, while ValidateSamFile did a more thorough analysis of the errors (plus also gives you warnings, has a long list of things it checks).
Edit: I saw that @genomax commented "use Picard ValidateSamFile" without making it an answer, so maybe it passes unattended to readers. I support that answer, but now at least I've registered a more thorough explanation of why that method is better than the other suggested ones.