Table 3 Overview of parameters evaluated for filtering SNPs. Vcftools test settings and subsequent ranges of investigated specifications are displayed
Test setting | Parameter | Tested range | Description |
|---|---|---|---|
1 | minDP | 2–16 (interval 2) | minimum read depth—allow only SNPs with given minimum read depth |
1 | max DP | 30–100 (interval 5) | maximum read depth—allow only SNPs with given maximum read depth |
2 | max-missing-count | 8–18 (interval 2) | maximum number of allowed missing genotypes—exclude SNPs with more than defined number of missing genotypes over all individuals |
2 | min-mean-DP | 10–30 (interval 2) | minimum mean read depths—allow only SNPs with at least the given mean read depth values over all individuals |