Package Function Criteria Scaffolds Variants Samples % missing data
78369 122605 94 51.54
SNPfiltR hard_filter min depth = 5 min genotype quality = 20 78369 122605 94 63.63
max_depth max depth = 137 (i.e. 2*SD) 59557 111893 94 66.41
min_mac minimum minor allele count = 3 27819 26918 94 44.94
filter_allele_balance min ratio = 0.2 max ratio = 0.8 27819 26918 94 31.33
filter_biallelic keep biallelic SNPs only 27819 26918 94 31.33
Custom script remove SNPs missing >5% data 4774 9849 94 1.63
minimum minor allele count = 3 4774 7492 94 1.63
retain SNPs with Ho < 0.6 4770 7485 94 1.63
SNPRelate snpgdsLDpruning method=”corr”, ld.threshold = 0.5, slide.max.bp = 500000, autosome.only = FALSE 4770 5239 94 1.61
Custom script Remove replicate samples and highly-related individuals 4770 5239 70 0.98
Remove sex-linked loci 4770 5239 70 0.98
tess3 & pvalue Remove loci under putative selection 4770 5239 70 0.98
gl.outflank Remove loci under putative selection 4770 5239 70 0.98