Dataset formats
The input dataset is in gd_snp format. The output is a composite dataset, containing both a text table and a PDF plot. (Dataset missing?)
What it does
This tool reports distributions of a SNP reliability indicator, in this case sequence coverage, for individuals or populations. The coverage can be computed for all individuals, a subset of individuals, or totals for populations defined by the Specify Individuals tool. The results are reported as a text table giving the cumulative distributions, and as a plot.
Example
input:
chr1 14929 A G 999 21 30 1 127 7 11 1 28 7 29 0 5 2 5 1 17 10 14 1 81 17 74 1 42 15 22 1 125 29 84 1 88 6 10 1 11 30 23 1 79 19 1 2 71 24 0 2 99 41 10 2 2 chr1 17451 C T 6.88 119 1 2 255 12 0 2 63 35 0 2 59 14 0 2 72 19 1 2 57 101 1 2 255 38 8 1 20 125 0 2 255 13 0 2 62 42 0 2 51 44 0 2 64 26 0 2 108 59 0 2 194 chr1 30922 G T 999 0 23 0 66 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 2 0 3 0 14 0 39 14 16 1 153 0 45 0 132 6 0 2 48 19 0 2 87 3 0 2 32 0 0 -1 0 0 0 -1 0 etc.
text output:
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 John West 0 0 0 0 0 0 0 0 1 1 1 1 2 2 3 3 4 4 5 6 NA12892 0 2 5 11 20 31 43 55 67 77 84 90 93 96 97 98 99 99 99 99 NA12891 0 0 0 0 0 1 1 2 3 5 6 9 11 15 19 23 29 35 41 47 NA12249 1 4 11 23 38 54 68 79 88 93 96 98 99 99 99 99 99 99 99 99 NA12342 0 0 1 1 2 4 6 9 13 18 23 29 36 43 50 58 65 71 77 82 KB1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 2 2 ABT 0 0 0 0 0 0 1 1 1 2 3 4 5 6 8 10 12 14 18 21 NA18507 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 NA19238 0 0 0 1 2 4 6 10 14 19 25 32 39 47 55 62 69 76 81 86 NA19239 0 0 0 0 1 1 2 4 5 8 11 15 19 24 31 37 44 51 58 65 YH 2 4 6 7 8 8 9 10 11 12 14 17 19 22 25 29 32 36 40 45 KOREAN 0 0 1 1 3 4 5 7 10 12 15 19 22 27 31 37 42 48 54 60 JPT 0 0 0 0 0 0 0 0 1 1 1 2 2 3 4 5 7 8 10 12 etc.
graphical output:
