Use references from CTAT

[rannick]

Description of feature

Use references from CTAT.
Allows to shorten reference building time and maybe call a few more fusions with STAR-fusion as it is optimised for this

[fevac]

I was wondering about this change. The clear benefit is the short reference building time but are the CTAT genomes up-to-date? I don't see many updates coming from them. Is that a problem?

[fevac]

The ensembl annotation is missing the superlocus IGH IGL so including the following in the reference gtf might improve their detection with starfusion and arriba

chr14	SuperLocus-ext	exon	105583731	106875071	.	-	.	gene_id "IGH.g@-ext"; transcript_id "IGH.t@-ext"; gene_name "IGH@-ext";
chr14	SuperLocus-ext	exon	105583731	106875071	.	+	.	gene_id "IGH-.g@-ext"; transcript_id "IGH-.t@-ext"; gene_name "IGH-@-ext";
chr22	SuperLocus-ext	exon	22030934	22923034	.	+	.	gene_id "IGL.g@-ext"; transcript_id "IGL.t@-ext"; gene_name "IGL@-ext";
chr22	SuperLocus-ext	exon	22030934	22923034	.	-	.	gene_id "IGL-.g@-ext"; transcript_id "IGL-.t@-ext"; gene_name "IGL-@-ext";