I am wondering if you could recommend me a pipeline to call SNPs from GBS data.
I see two principal alternatives:
1.- Demultiplexing, filter raw reads, mapping to a reference genome, preprocessing the alignment files, and call SNPs with GATK or samtools or other sofware.
2.- Use TASSEL or FAST-GBS or another software designed for this.
I am wondering if some one have experience with these two approaches. Call SNPs carrying all the steps such as in WGS or use a special pipeline for GBS. Which is better?