ChaissonLab/danbing-tk: danbing-tk v1.3.1 (manuscript)

This version is associated with the manuscript: "The motif composition of variable-number tandem repeats impacts gene expression"

Changes:

• Updated preferred usage of danbing-tk by turning on kmer filter: -kf 4 1
• Reduces kmer output size by saving only counts, and uses index file to reconstruct locus name and kmer names

Additional resource on Zenodo:

• VNTR statistics and annotations on 35 HGSVC assemblies
• GTEx gene-level eVNTR discoveries
• GTEx gene-level eMotif discoveries
• GTEx fine-mapping results using susieR
• Bias matrices for HGSVC, HPRC, GTEx, and Geuvadis samples used in bias correction
• GTEx bias-corrected kmer dosage table
• Geuvadis bias-corrected kmer dosage table

Additional analysis scripts for bias correction, eQTL mapping, and fine-mapping are available in this repo.