Radseq analysis projects scripts
1.processradtags.sh Load Stacks Run Process radtags. We already ran trimscript.sh to clean reads and trim to correct length so this script should be quick, we should not loose many reads and makes sure all files are in correct format for refmap.pl Stacks
2.BWA to BAM Load BWA and SAMtools Index reference genome and run BWA MEM on all your samples
3.Stacks refmap.pl Load Stacks Using reference genome - make sure reference genome is indexed see script (BWA index) 4.Stacks Populations.sh -Careful of filtering options to make the next step easier
Load VCFtools Filter VCF to set criteria i.e Missing data
Remove outliers from PCAdapt and Bayescan
Structure/ FastStructure and running these programs in Structure_Threader
Fineradstructure
Dsuite
Treemix
Bayescan
PCAdapt