@Maxime Garcia We were wondering if the plans (in the future) are also to support Panel of Normals for CHM13 and long-read sequencing pipelines. We got some panel of normals that we want to use for tumour-only variant calling with ClairS-TO for instance that are too large to host on github. Maybe these can be hosted on aws and included in the end as well?

That sounds like a good idea

Did make an issue but wanted to inquire quickly if you know if there's a way for us to host it/speed up the hosting on AWS? We would like to implement it for our 1.0.0 release but not sure where to host files this size (and don't want to push you to do it hehe)

What tools do you need indexes for, on top of the genome itself?

Not sure if I fully understand but this PoN will be used for tumour only short variant calling, so

Mutect2

(short-read) and

ClairS-TO

(long-read) is what I can think off on the top of my head. Maybe @Robert Forsyth can add to this?

They should be easily recyclable, they're based directly off ClairS-TO's panel of normal files they use for gr38, but they're not specifically designed for use in that tool