Re-analysis of chromatin accessibility QTLs from the Kumasaka et al, 2018 study

ATAC-seq data from Kumasaka et al, 2018 was processed with the nf-core/atacseq v2.1.2 pipeline using Nextflow v23.09.3. We aligned raw ATAC-seq reads to the GRCh38 reference genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa downloaded from Ensembl) with BWA v0.7.17. We called broad peaks with MACS2 v2.2.7.1 and defined consensus peaks as the union of all peaks that were present in at least 5% of the samples. We then quantified read overlaps with the set of consensus peaks with featureCounts v2.0.1. Finally, we normalised the read counts (counts per million) and then used the inverse normal transformation to standardise the data distribution.

Genotype data for the 91 overlapping samples were downloaded from 1000 Genomes 30x on GRCh38 website. Finally, we used the eQTL-Catalogue/qtlmap v24.01.1 workflow to perform chromatin accessibility QTL analysis. We set cis window size to 200,000 bp and excluded peaks that had less than 25 variants within that window. More details of the association testing workflow can be found here.