help recovering data from bam w/ bad header

[jmartin]

I have a bam file that I need to work with to reproduce an issue for some troubleshooting. This bam file was left by a student in a collaborator's lab and we pretty much only have this bam file (no upstream or downstream derivatives of the file). Samtools view gives this error message:

[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "7_2.bam".

Picard's ValidateSamFile produces only the message:

ERROR: Read groups is empty
SAMFormatException on record 01

along with STDERR that looks like the java code is erroring out. Bamtools stats gives this error:

bamtools stats ERROR: could not open input BAM file(s)... Aborting.


This file is of a size that would be appropriate for the mapping done, and somehow the person who created it used it. It is a rather old copy that has now been passed around a bit but if it was truncated from a transfer I'd have expected different errors (I think...).

Is there some way I can dump just the data from a bam file without dealing with the bad header? Or is there some way I can read in a generic 'dummy' header over the bad one to save the data?


Thanks,
John

[dpryan]

How's your C programming? I suspect you're going to have to code something with htslib to figure out (A) where the problem is and (B) get around it as best as possible.

[jmartin]

I've no experience with C coding, I mainly stick to scripting languages (perl & python). But I'll take a look at the htslib methods and see if I can muddle through.

Thanks,
John

[r.rosati]

Does this help?

https://gatkforums.broadinstitute.org/gatk/discussion/7571/errors-in-sam-bam-files-can-be-diagnosed-with-validatesamfile

[jmartin]

I'll try the GATK ValidateSamFile and see what it says. GATK tools usually do give helpful error messages and I haven't tried that one yet.

Thanks,
John