Supplemental Material for Hawley et al., 2025
dataset
posted on 2025-03-03, 19:31 authored by R. Scott Hawley, Andrew Price, Hua Li, Madhav Jagannathan, Cynthia Staber, Stacie E. Hughes, Stefanie Williams, Anoja Perera, Rhonda R. Egidy, Amanda Lawlor, Danny E. Miller, Justin P. BlumenstielDeepVariant vcf files containing mutations against the D. mauritiana reference genome generated using the below methods:
After sequencing, raw fastq files were adapter trimmed using Trim Galore (v0.6.10) and aligned to the D. mauritiana reference genome (D_mauritiana_ASM438214v1; RefSeq) using bwa mem (v0.7.17). Aligned reads were then deduplicated by processing them through samtools (v1.18) fixmate, sort, and markdup with the -r argument. Variant calling was run on these deduplicated reads using deepvariant (v1.5.0) with the Whole Genome Sequence (WGS) model type argument
