bamsort - SO:coordinate not being added to @HD line about biobambam2

[gt1]

Hi Angela,

bamsort so far only ever updated an existing sort order tag but never added one by itself. I have changed this in the latest release (2.0.31). Could you please check whether this works better for you?

Thanks
German

[amatchan]

Hi German,
thanks for the quick reply.
Yes I've just done some further checking and can see that the STAR command outputs a BAM with just this in the header line to start with:
@hd VN:1.4

If I manually rehead the file with samtools reheader to add: SO:unsorted, then bamsort will work.
I'm constrained to using v2.0.25 in our production environment at the moment but I should be able to at least modify the input BAM to add the SO:unsorted tag.

I'll test v 2.0.31 and, if that works, will request that our system moves to that asap.

Thanks very much
Angela