Mandatory for GTF to be gene-collapsed before entering the annotation_coord for phenotype file

[hsun3163]

As it turn out. The gene.gtf file provided in out snuc study is exon based instead of gene based. This create a lot of records with duplicates gene IDs but different start-end position and may leads to incorrectly labeled bed file.

Therefore, from a workflow perspective, the gtf needs to be preprocessed via the collapsed gene module.