title: WGS:Drosophila:efas2Bergstralh
design: Analysis was performed with help from the University of Missouri bioinformatics core. Raw reads were filtered by fastp (Chen et al. 2018). The clean reads were used for mapping and variant calling, which was performed using the Parabricks pbrun germline command with the Drosophila reference genome GCF_000001215.4 (NCBI). Variants were subsequently hard-filtered by GATK VariantFiltration following its best practice (Franke and Crowgey 2020). The VCF file nexus.all-chrs.vars.AN268.R6.share.verboseINFO.vcf.gz (FlyBase Associated Files, updated 11-27-23), which contains updated Drosophila melanogaster genetic variant data, was used to identify reported/common variants. BAM files were visualized using IGV (Robinson et al. 2023).