annotate prepare_population_structure.xml @ 19:fa34d259eb8f

Removed unicode from Fst_ave.c
author miller-lab
date Tue, 23 Oct 2012 14:37:26 -0400
parents f04f40a36cc8
children 248b06e86022
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Filter and convert to the format needed for these tools</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
5 prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
6 #if $individuals.choice == '0'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
7 "all_individuals"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
8 #else if $individuals.choice == '1'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
9 #for $population in $individuals.populations
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
10 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
11 "$pop_arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
12 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
13 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
14 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
15 #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
16 "$arg"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
17 #end for
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
18 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
19
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
20 <inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
21 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
22 <conditional name="individuals">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
23 <param name="choice" type="select" label="Individuals">
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
24 <option value="0" selected="true">All individuals</option>
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
25 <option value="1">Specified populations</option>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
26 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
27 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
28 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
29 <repeat name="populations" title="Population" min="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
30 <param name="p_input" type="data" format="gd_indivs" label="Individuals" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
31 </repeat>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
32 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
33 </conditional>
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
34 <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
35 <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
36 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
37 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
38
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
39 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
40 <data name="output" format="gd_ped">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
41 <actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
42 <action type="metadata" name="base_name" default="admix" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
43 </actions>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
44 </data>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
45 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
46
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
47 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
48 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
50 <param name="min_reads" value="3" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
51 <param name="min_qual" value="30" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
52 <param name="min_spacing" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
53 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
54 <output name="output" file="test_out/prepare_population_structure/prepare_population_structure.html" ftype="html" compare="diff" lines_diff="2">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
55 <extra_files type="file" name="admix.map" value="test_out/prepare_population_structure/admix.map" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
56 <extra_files type="file" name="admix.ped" value="test_out/prepare_population_structure/admix.ped" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
57 </output>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
58 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
59 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
60
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
61 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
62
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
63 **Dataset formats**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
64
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
65 The input datasets are in gd_snp_ and gd_indivs_ formats.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
66 The output dataset is in gd_ped_ format. (`Dataset missing?`_)
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
67
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
68 .. _gd_snp: ./static/formatHelp.html#gd_snp
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
69 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
70 .. _gd_ped: ./static/formatHelp.html#gd_ped
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
71 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
72
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
73 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
74
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
75 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
76
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
77 This tool converts a gd_snp dataset into the format needed for estimating
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
78 the population structure. You can select the individuals to be included,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
79 by using "population" datasets created via the Specify Individuals tool.
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
80 (It is important for these population datasets to have distinguishable names,
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
81 since they will be stored in the output's metadata so that subsequent tools
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
82 can use them as labels. If necessary, rename the datasets to give them
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
83 distinct and meaningful names before running this tool.)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
84
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
85 You can also filter the SNPs, based on criteria such as minimum coverage
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
86 (a qualifying SNP must have at least this many reads for every included
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
87 individual), minimum quality score (for every included individual), and/or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
88 minimum spacing (SNPs that are too close together on the same chromosome or
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
89 scaffold are discarded). In addition to producing the filtered and formatted
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
90 .map and .ped files for subsequent analysis, the tool reports the number of
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
91 SNPs meeting these conditions, which can be seen by clicking on the eye icon
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
92 in the history panel after the program runs.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
93
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
94 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
95
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
96 **Example**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
97
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
98 - input::
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
99
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
100 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
101 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
102 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
103 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
104
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
105 - output cover page::
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
106
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
107 Prepare to look for population structure Galaxy Composite Dataset
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
108 Output completed: 2012-10-01 04:09:36 PM
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
109
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
110 Outputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
111 * admix.ped (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
112 * admix.map (link)
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
113 * Using 222 of 400 SNPs
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
114
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
115 Inputs
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
116 * Minimum reads covering a SNP, per individual: 6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
117 * Minimum quality value, per individual: 0
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
118 * Minimum spacing between SNPs on the same scaffold: 0
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
119
18
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
120 Populations
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
121 * Pop. A
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
122 1. PB1
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
123 2. PB2
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
124 * Pop. B
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
125 1. PB3
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
126 2. PB4
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
127 * Pop. C
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
128 1. PB6
f04f40a36cc8 Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
129 2. PB8
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
130
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
131 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
132 </tool>