LINDTIE Reference Dataset: Human hg38 + CHESS v3.0

This dataset contains compressed archives of pre-built human reference files (derived from hg38 and CHESS v3.0) and the processed COSMIC database required to run the LINDTIE aberrant transcript variant caller. The tar archive includes the nine reference files used by LINDTIE: chess3.0.fa chess3.0.gtf chess3.0.info Cosmic_CancerGeneCensus_v103_GRCh38_tier.tsv gencode.v49.primary_assembly.annotation.gtf hg38.fa hg38.fa.fai hg38_splice_junctions.bed tx2gene.txt After downloading, extract the tar file; this will create a ref directory containing all the required reference files. Move or place the ref directory into the LINDTIE base directory.