2bRAD-GATK

DOWNLOAD THE LATEST UPDATES FROM https://github.com/z0on/2bRAD_GATK



2bRAD is a method for cost-efficient whole-genome genotyping described in Wang et al 2012
http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html

This project is about analyzing 2bRAD data using a genome reference (could be a species from the same genus).

Scripts and walkthrough for:
- trimming and quality filtering;
- removing PCR duplicates;
- mapping to genome reference;
- realigning around indels;
- base quality score recalibration;
- calling variants;
- variant quality score recalibration based on genotyping replicates;
- smart-thinning and final filtering;
- quality assessment based on replicates.

also included are walkthroughs for analysis:
- generating data for genome scans (Fst, BayeScan, pi, Tajima's D, deviations in Linkage Disequilibrium)
- ADMIXTURE