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
[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
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