Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

BioRxiv DOI: https://doi.org/10.1101/2024.04.16.589693

This repository hosts the scripts utilized for generating and analyzing the shared polymorphism dataset of Daphnia species.

Author:

Connor S. Murray
Email: csm6hg@virginia.edu

Script Repository:

Figures:

Contains the main figures along with data and scripts used for plotting.

Supplemental:

Contains supplemental figures, tables, data, and associated scripts.

VCF Generation:

This section encompasses the pipeline for generating Variant Call Format (VCF) files:

• VCF Creation:

  • Downloading short-read Illumina fastqs.
  • Mapping to European Daphnia pulex genome.
  • BAM generation and merging.
  • HaplotypeCaller, GATK processing, merging, and SNP calling.
  • VCF and genomic data structure (GDS) generation.

• VCF Filtration:

  • Filter to benchmark universal single-copy ortholog (BUSCO) genes.
  • Multi-locus genotype (MLG) classification.
  • Filtering SNPs based on recommendations for species lacking reference SNP panels.

• Quality Control:

  • Missingness, quality scores, coverage, and MultiQC on BAMs.

• Read Based Phasing

  • WhatsHap phasing of samples and phased VCF creation.

• Lift Over

  • LiftOver of European and North American Daphnia pulex genomes.
  • Repeat masking, single-copy orthologous genes, and genotype concordance.