Variant calling in the Goldilocks Zone: how reference genome choice and read mapping stringency impact heterozygosity estimates and phylogenetic analyses

This archive includes a short read dataset mapped to different references using different mapping methods, the scripts and summary statistics for evaluating the efficiency and accuracy of mapping, the heterozygosity, and tree topology resulting from each reference and method. 
, , # Data and Scripts for Mohn, Garner, Manos, Hipp. Variant calling in the Goldilocks Zone: how reference genome choice and read mapping stringency impact heterozygosity estimates and phylogenetic analyses.

Molecular Ecology Resources.

## Data and files

### rubra_bt2_e2e.vcf.gz

VCF file of bases called against the Q. rubra reference using Bowtie 2 --end-to-end

### rubra_bt2_local.vcf.gz

VCF file of bases called against the Q. rubra reference using Bowtie 2 --local

### rubra_bwa.vcf.gz

VCF file of bases called against the Q. rubra reference using BWA

### alba_bt2_e2e.vcf.gz

VCF file of bases called against the Q. alba reference using Bowtie 2 --end-to-end

### alba_bt2_local.vcf.gz

VCF file of bases called against the Q. alba reference using Bowtie 2 --local

### alba_bwa.vcf.gz

VCF file of bases called against the Q. alba reference using BWA

### lobata_bt2_e2e.vcf.gz

VCF file of bases called against the Q. lobata reference using Bowtie 2 --end-to-end

### lobata_bt2_local.vc...,