LINDTIE Reference Dataset: Human hg38 + CHESS v3.0 + Viral reference

This dataset contains compressed archives of pre-built human reference files (derived from hg38 and CHESS v3.0) merged with viral references (including HTLV1, HPV, HBV, HIV1, HIV2, EBV), and the processed COSMIC database required to run the LINDTIE aberrant transcript variant caller.

The tar archive includes the seven reference files used by LINDTIE:

• chess3.0_with_HTLV1_HPV_HBV_HIV1_HIV2_EBV.fa
• chess3.0_with_HTLV1_HPV_HBV_HIV1_HIV2_EBV.gtf
• chess3.0_with_HTLV1_HPV_HBV_HIV1_HIV2_EBV.info
• Cosmic_CancerGeneCensus_v103_GRCh38_tier_fusion.tsv
• hg38_splice_junctions.bed
• hg38_with_HTLV1_HPV_HBV_HIV1_HIV2_EBV.fa
• 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.