Structural variant VCF files of Drosophila melanogaster inbred strains from Hemker et al. 2026

The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the effect of the length of long-reads on automated variant callers is not well understood, especially for non-human species. We used Oxford Nanopore Technologies to long-read sequence eight, inbred D. melanogaster strains to extremely high coverage (mean 238x, and we then downsampled the reads to create read pools of different length distributions. Here are the VCFs representing the structural variant calls from each of these read-length distributions. Description of the data and file structure Eight inbred D. melanogaster strains were deeply sequenced (mean: 238x) with nanopore long reads. These read pools were then computationally downsampled into five pools of distinct read-length distributions and coverages. Each of these pools were additionally assembled into genomes. For each read-length distribution we called structural variants using the same procedure. For each strain, five callers were used to find structural variants. These variants were kept if they were found by at least two callers. The eight strain VCFs were then merged together to create a population VCF. Finally, the VCF were filtered to keep structural variants located in D. melanogaster euchromatin. For the short-read data, we used four read-based callers, but all other steps were the same.Files and variablesFile: ultra-long-20x.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the ultra-long 20x-coverage read-length distribution.File: ultra-long-10x.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the ultra-long 10x-coverage read-length distribution.File: ultra-long.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the ultra-long 30x-coverage read-length distribution.File: standard.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the standard read-length distribution.File: minimum-10kb.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the minimum-10kb read-length distribution.File: short-read.population.euchromatic.vcf.gz Description: Population-level structural variant calls in euchromatin for the short-read-length distribution.Code/software The VCFs can be most easily viewed and manipulated with bcftools. The VCFs were compressed with bgzip. We recommend visualizing the VCFs in Jbrowse2, which has structural variant support. The VCFs can also be uploaded as tracks to the UCSC Genome Browser to find overlap with other annotated genomic elements.