Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties_Campanian_clones
The VCF file includes the Campanian clones CAMAIOLA n. (n. 20), AGLIANICO LASCO (n.64), and GRECO B. (n. 24), genotyped by dd-RADseq approach.
Steps to reproduce
Campanian genetic material was genotyped using ddRADseq (Peterson et al., 2012). The ddRADseq tags were aligned to the reference genome GCA_000003745.2 (Pinot Noir, PN40024) using BWA-MEM (Li and Durbin, 2009). The gstacks and populations (with options -R = 0.75 and --max-obs-het = 0.8) utilities included in Stacks v2.53 (Catchen et al. 2013) were used for SNP calling and for applying filtering options.