GTEx runs

Flux Version

Flux-Capacitor v1.2.3 (Flux Library: 1.20)

Annotation File

(Broad version, check for stable URL or upload)

Parameter File

ANNOTATION_FILE gencode.v12.annotation.patched_contigs_sorted.gtf 
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING AUTO

Command Line

flux-capacitor -p <parameter_file> -i <sample.bam> -o <output.gtf>