A bovine long read cohort to identify SVs and quantify their impact on gene expression

This dataset contains small and structural variants identified from HiFi sequencing of 117 bulls of predominant Braunvieh ancestry.

This repository contains the following data

• VCF used for association mapping
  • final.117.vcf.gz
• TPM matrices (unfiltered and filtered/normalized)
  • TPM_gene_testis_UNFILTERED.tsv
  • TPM_gene_testis_FILTERED_NORM.tsv
• PSI/splicing matrices (unfiltered counts and filtered/normalized PSI)
  • hifi_testis_perind_numers.counts.gz
  • all.leafcutter.bed
• eQTL and sQTL results (conditional = summary stats after conditional testing for significant variant-phenotype pairs)
  • eQTL: eQTL_conditional.txt.gz
  • sQTL: sQTL_conditional.txt.gz
• covariates (covariates used for eQTL and sQTL mapping)
  • covariates_TPM.txt
  • covariates_PSI.txt
• A cross-table (HiFi_cohort_accession_numbers_zenodo.xlsx)to assign individual IDs to ENA accession IDs.

The bovine ARS-UCD2.0 assembly and the Refseq annotation (release 106) were used