Verifying BAM Header

Question

[sbilobram]

Recently some of our BAMs have come through with duplicate SQ tags in the headers. This caused some of the downstream tools to fail. We now want a tool to check that the BAMs' headers conform to SAM/BAM Format specs. The Picard/GATK ValidateSamFile fails on these BAMs but gives an useful error message. The samtools quickcheck does not find this malformation.

IS THERE A TOOL THAT WILL CHECK THAT A BAM HEADER IS VALID?

[Pierre Lindenbaum]

The samtools quickcheck does not find this malformation.

samtools quickcheck does not SEARCH this malformation.

[Pierre Lindenbaum]

IS THERE A TOOL THAT WILL CHECK THAT A BAM HEADER IS VALID?

what's wrong with ValidateSamFile ?

[Pierre Lindenbaum]

even samtools will display a warning:

samtools view -H toy.bam | awk '/^@SQ/ {print} {print}' |  samtools view -H  > /dev/null
[W::sam_hdr_parse] duplicated sequence 'ref'
[W::sam_hdr_parse] duplicated sequence 'ref2'

[sbilobram]

yeah this is great but we want to capture any/all mal formed Headers. If I didn't know this header had duplicate SQ tags I wouldnt not have known to search for '/^@SQ/

[Pierre Lindenbaum]

what do you mean with

but we want to capture any/all mal formed Headers.

just detect the error and dump the header with samtools view -H (?)

[sbilobram]

We want a tool that would detect any error in the BAM header not just duplicated SQ tags

[sbilobram]

ValidateSamFile crashes with an error. The error is helpful but the tool does stop running which we dont really want.

[Pierre Lindenbaum]

I'm sorry but sounds like "the car has no wheels, it's broken, but we want it to drive"