T2T reference

Question

T2T reference

Closed this issue a year ago · 1 comments

Hi!

I have recently aligned WGS of human tumour to the T2T-CHM13v2.0 reference genome and am hoping to call somatic SVs.
Is GRIDSS2 compatible with the T2T reference?

Thanks for your help :)

Answer 1 · 2023-08-15T05:42:13.000Z

GRIDSS2 is not tied to any specific reference genome so should work with that T2T reference without issue.

GRIDSS2 requires some additional files which are generated from the reference (e.g. a bwa index) so make sure the first time you run GRIDSS against a new reference you only run one instance of GRIDSS. Having multiple processing creating a bwa index at the same time will result in a corrupted index.