DOI: 10.5061/dryad.fttdz0964
title: Variant calling in the Goldilocks Zone: how reference genome choice and read mapping stringency impact heterozygosity estimates and phylogenetic analyses

description: 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. 
description: # 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.vcf.gz VCF file
 of bases called against the Q. lobata reference using Bowtie 2 --local ###
 lobata_bwa.vcf.gz VCF file of bases called against the Q. alba reference
 using BWA ### mongolica_bt2_e2e.vcf.gz VCF file of bases called against
 the Q. mongolica reference using Bowtie 2 --end-to-end ###
 mongolica_bt2_local.vcf.gz VCF file of bases called against the Q.
 mongolica reference using Bowtie 2 --local ### mongolica_bwa.vcf.gz VCF
 file of bases called against the Q. mongolica reference using BWA ###
 ReferenceGenomeTest_v1.0.Rmd this file is an R markdown file for analyzing
 the summary statistics and generating the figures for this manuscript it
 reads the files in the inputFiles folder and exports the figures as pdfs
 to the outputFiles folder ### inputFiles.zip this is a folder with all the
 needed input files to run the ReferenceGenomeTest_v1.0.rmd file ####
 alb_bt2-l.tre.treefile tree from the concatenated matrix of samples mapped
 to the Quercus alba reference genome using Bowtie2 --local ####
 alb_bt2_e2e.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus alba reference genome using Bowtie2 --end-to-end
 #### alb_bwa.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus alba reference genome using bwa mem ####
 lob_bt2-l.tre.treefile tree from the concatenated matrix of samples mapped
 to the Quercus lobata reference genome using Bowtie2 --local ####
 lob_bt2_e2e.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus lobata reference genome using Bowtie2 --end-to-end
 #### lob_bwa.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus lobata reference genome using bwa mem ####
 mong_bt2-l.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus mongolica reference genome using Bowtie2 --local
 #### mong_bt2_e2e.tre.treefile tree from the concatenated matrix of
 samples mapped to the Quercus mongolica reference genome using Bowtie2
 --end-to-end #### mong_bwa.tre.treefile tree from the concatenated matrix
 of samples mapped to the Quercus mongolica reference genome using bwa mem
 #### rub_bt2-l.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus rubra reference genome using Bowtie2 --local ####
 rub_bt2_e2e.tre.treefile tree from the concatenated matrix of samples
 mapped to the Quercus rubra reference genome using Bowtie2 --end-to-end
 #### rub_bwa.tre.treefile_fixed tree from the concatenated matrix of
 samples mapped to the Quercus rubra reference genome using bwa mem ####
 Stats3.xlsx an excel file with the statistics and data on each sample and
 reference genome. The "HetMissing" tab consists of
 heterozygosity and missing sites derived from vcftools output. The
 "AssemblyStats" tab consists of values data output from Bowtie2
 or Samtools. The "BranchLengths" tab values were derived from
 the IQ-TREE2 topologies. Finally the "Samples" tab contains
 information also available on NCBI about the specimens. ####
 taxa_trans_table.txt a file with names for renaming species tree data ###
 bt2_endtoend_script.txt Script for processing reads post chloroplast
 filtering via Bowtie 2 --end-to-end to statistic calculation ###
 bt2_local_script.txt Script for processing reads post chloroplast
 filtering via Bowtie 2 --end-to-end to statistic calculation ###
 bwa_script.txt Script for processing reads post chloroplast filtering via
 Bowtie 2 --end-to-end to statistic calculation