filtered SNP set used for population structure and clustering analysis

These SNPs were called from 109 Metchnikowia sp whole genomes mapped to MR_a10 reference genome using GATK best practices guidelines. Hard filtering of initial SNPs was performed using the GATK variant filtration tool (v3.4) and VCFtools (v1.5) as per best practices (Danecek et al. 2011), using the following parameters: base quality = 20, quality by depth = 2.0, mapping quality = 30, Fisher strand bias = 60, mapping quality rank sum =-12.5, and ReadPosRankSum = -8.0. Post InDel removal, the SNP set consisting 1.27 million SNPs across 109 strains was further filtered to exclude: non-bi-allelic SNPs, a minor allele frequency below 0.05 and polymorphisms with more than 50% missing data. To resolve SNPs in linkage, a window size of 50 SNPs advanced by 5 SNPS at a time and an r2 threshold of 0.5 was used. The final set of high confidence SNPs consisted of 88, 192 polymorphisms. See attached scripts.