Scripts for analyzing my 2bRAD data from corals in French Polynesia (modified from Dr. Mikhail Matz's scripts at https://github.com/z0on/2bRAD_denovo)
Head straight to the 'walkthrough' files for each part for instructions.
Part 1: Genome
Placing & indexing reference genome - if you don't have a reference genome you'll have to follow Misha's instructions at https://github.com/z0on/2bRAD_denovo, the rest of my instructions will also be missing any 'de novo' specific commands
Part 2: Reads
Filtering & trimming raw reads
Mapping reads to reference genome to create .bam files
Part 3: Population structure
First, use angsd + ibs results to identify technical replicates & clones. Then use vcftools to find average site depth per sample. Then re-run angsd without worst samples & without technical replicates/clones. Explore population structure in PCA & K plot.
Part 4: FST outliers
Using .vcf file to find FST outliers using Bayescan