Scripts and commands detailed here used for validation of DGRP (Drosophila Genetic Reference Panel) and DPSE (Drosophila pseudoobscura) lines. Both scripts are very similar to each other and contain extensive comments on usage of commands within.
Using the scripts necessitates installing bcftools, bedtools, and seqkit first. In addition to the instructions provided in those links, bcftools and bedtools can be installed through Anaconda. bcftools can also be installed via Homebrew.
Both scripts utilize specific VCF and reference FASTA genomes. For DGRP the VCF file can be downloaded here directly from DGRP. The reference FASTA file can be downloaded directly from UCSC Genome Browser here. Both links will download the file immediately upon clicking.
For DPSE the VCF file was produced in-house by Madison Watkins. The page for the reference FASTA file can be found on NCBI. This will not immediately download the file, though NCBI provides the following curl command to download a folder containing the file on that page:
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_009870125.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_009870125.1.zip" -H "Accept: application/zip"
This repository is part of the following publication: Shiran MG, Bailey NP, McCann L, Rivera-Rincón N, Saurette E, Stevison LS. 2026. Efficient RFLP-based Protocol for Routine Authentication of Drosophila. microPublication Biology. 10.17912/micropub.biology.001949
The DOI for citing this repository is:
