Realigned BAM not sorted about octopus

[dancooke]

Hi Chris,

Thanks for opening an issue on this. I am aware of this problem, but unfortunately haven't had the time to try to resolve it yet, and I didn't want to delay v0.5.0-beta any longer.

The problem is not specifically to do with tumour BAMs; Octopus doesn't distinguish samples in any way when realigning BAMs - it just considers the called genotypes. I think the problem is linked to the way Octopus realigns reads in blocks that correspond to phase sets.

I'll try to resolve this as soon as possible, but my focus is on finishing a manuscript for Octopus now, so it might be a few weeks.

Thanks,
Dan

[ChristopheLegendre]

@dancooke
Hi Dan,

Thanks for your reply; I noticed the issue when I tried to load the BAM file in IGV;
Just wanted to give feedback and make users aware of it.
No rush; The users can still manually sort and index the bam files ;-) :-)

Wish you well with the manuscript.

Best,
Chris

[dancooke]

I think that I've fixed this in f0b49cf, which is available on the develop branch and will appear in the next release. Please re-open if any further issues.