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GTEx runs

Flux Version

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

Annotation File

http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/examples/reference/Homo_sapiens_assembly19.fasta.gz

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>
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