Genomic variant data and codes used for analysis in the manuscript - Whole genome sequencing reveals the structure of environment associated divergence in a broadly distributed montane bumble bee, Bombus vancouverensis

See below for details of the files included below.

delly_vanc.vcf.gz # Raw output of Delly 

b.vanc.fully.filtered.100k.plus.recode.vcf.gz # output of freebayes which was filtered using VCFtools  v0.1.13 (Danecek et al. 2011) with the following flags: --remove-indels --min-alleles 2 --max-alleles 2 --minQ 20 --minDP 4 --max-missing 0.75

#Above file was also filtered to remove sites with unusually high coverage (>2x mean coverage) or excess heterozygosity. Finally SNPs that fell on scaffolds less than 100kb in length were removed

b.vanc.fully.filtered.100k.plus.recode.maf05.recode.ANN.vcf.gz #Fully filtered variant file (see manuscript for details) with annotation information

b.vanc.fully.filtered.100k.plus.recode.maf05.recode.impute.vcf.gz #Fully filtered variant file (see manuscript for details) after imputation with beagle 

#### Description of each script contained in this directory ####

Trim_N_QC.sh #Trim raw sequencing data and run fastQC to evaluate trimmed data

BWA_PICARD_vanc1.sh #Example of script used to align sequence data to the reference genome using BWA. Also, uses Picard tools to sort, deduplicate and index bam files

P_call_test-2-vanc.sh #First part of pipeline for calling SNPS with freebayes (calls freebayes-parallel-part1_vanc.sh)

freebayes-parallel-part1_vanc.sh #see above

Filter_vanc.sh #Create list of SV's to filter from DELLY output

filter_delly.sh #filter based on generated list of SV's 

delly_vanc.sh #call SV's using DELLY

bcf2vcf.sh # convert bcf from DELLY to vcf format 

freebayes-parallel-part2.sh #Second part of freebayes pipeline

merge_vanc_vars.sh #Second part of freebayes pipeline (calls freebayes-parallel-part2.sh)

site_depth_vanc.sh #Gets site depth per SNP

remove_highdepth_vanc.sh #removes SNPs above depth threshold

hardy_vanc.sh #calculates HWE per SNP

remove_hwe_vanc.sh #removes SNPs based on HWE threshold

filter_vcf_size.sh #Removes SNPs on scaffolds less than 100Kb in size

filter_vcf_maf05.sh #filters SNPs based on 5% MAF filter

beagle.sh #imputes using beagle 

LEA_con.R #converts vcf file into LFMM and geno format 

Snpeff_ANN.sh # annotate vcf file using SNPeff

plink_for_sambaR.sh # convert vcf file into format ready for use in sambaR

LD_test.sh #example of script used to calculate LD per scaffold 

vcf_stats.sh #Gets various stats from final filtered vcf 

get_pi_diversity.sh #gets per population nucleotide diversity 

sambaR.R #Runs SambaR

lfmm2_analysis.R #Code for running analysis on output of LFMM2 and generating graphs

Max_ent_map.R #Generates maxent map

RDA_script.R #Code for RDA analysis of structural variants 

snprelate_script.R #runs SNPrelate as well as makes graphs of Fst and pi along scaffolds of interest

repeat_correctedfst.R #Analysis for correlation between repeat density and Fst 

LD_script.R #analysis of linkage