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comparison average_fst.xml @ 22:95a05c1ef5d5

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update to devshed revision aaece207bd01
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 11 Mar 2013 11:28:06 -0400
parents d6b961721037
children 248b06e86022
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21:d6b961721037 22:95a05c1ef5d5
1 <tool id="gd_average_fst" name="Overall FST" version="1.1.0"> 1 <tool id="gd_average_fst" name="Overall FST" version="1.2.0">
2 <description>: Estimate the relative fixation index between two populations</description> 2 <description>: Estimate the relative fixation index between two populations</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 average_fst.py "$input" "$p1_input" "$p2_input" "$data_source.ds_choice" "$data_source.min_value" "$discard_fixed" "$output" 5 average_fst.py "$input" "$p1_input" "$p2_input" "$data_source.ds_choice" "$data_source.min_value" "$discard_fixed" "$output"
6 #if $use_randomization.ur_choice == '1' 6 #if $use_randomization.ur_choice == '1'
19 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" /> 19 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" />
20 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" /> 20 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" />
21 21
22 <conditional name="data_source"> 22 <conditional name="data_source">
23 <param name="ds_choice" type="select" format="integer" label="Frequency metric"> 23 <param name="ds_choice" type="select" format="integer" label="Frequency metric">
24 <option value="0" selected="true">sequence coverage</option> 24 <option value="0">sequence coverage</option>
25 <option value="1">estimated genotype</option> 25 <option value="1" selected="true">estimated genotype</option>
26 </param> 26 </param>
27 <when value="0"> 27 <when value="0">
28 <param name="min_value" type="integer" min="1" value="1" label="Minimum total read count for a population" /> 28 <param name="min_value" type="integer" min="1" value="1" label="Minimum total read count for a population" />
29 </when> 29 </when>
30 <when value="1"> 30 <when value="1">
93 93
94 Finally, the user decides whether to use randomizations. If so, then the user specifies how many randomly generated population pairs (retaining the numbers of individuals of the originals) to generate, as well as the "population" of additional individuals (not in the first two populations) that can be used in the randomization process. 94 Finally, the user decides whether to use randomizations. If so, then the user specifies how many randomly generated population pairs (retaining the numbers of individuals of the originals) to generate, as well as the "population" of additional individuals (not in the first two populations) that can be used in the randomization process.
95 95
96 The program prints the following measures of FST for the two populations. 96 The program prints the following measures of FST for the two populations.
97 97
98 1. The formulation by Sewall Wright (average over FSTs for all SNPs). 98 1. The Reich-Patterson estimator (average over FSTs for all SNPs).
99 2. The Weir-Cockerham estimator (average over FSTs for all SNPs). 99 2. The population-based Reich-Patterson estimator.
100 3. The Reich-Patterson estimator (average over FSTs for all SNPs). 100 3. The formulation by Sewall Wright (average over FSTs for all SNPs).
101 4. The population-based Reich-Patterson estimator. 101 4. The Weir-Cockerham estimator (average over FSTs for all SNPs).
102 102
103 If randomizations were requested, it prints a summary for each of the four definitions of FST that includes the maximum and average value, and the highest-scoring population pair (if any scored higher than the two user-specified populations). 103 If randomizations were requested, it prints a summary for each of the four definitions of FST that includes the maximum and average value, and the highest-scoring population pair (if any scored higher than the two user-specified populations).
104 104
105 References: 105 References:
106 106
121 **Example** 121 **Example**
122 122
123 - output:: 123 - output::
124 124
125 Using 37847 SNPs, we compute: 125 Using 37847 SNPs, we compute:
126 Average Reich-Patterson FST is 0.31012.
127 The population-based Reich-Patterson Fst is 0.33625.
126 Average Wright FST is 0.22810. 128 Average Wright FST is 0.22810.
127 Average Weir-Cockerham FST is 0.30813. 129 Average Weir-Cockerham FST is 0.30813.
128 Average Reich-Patterson FST is 0.31012.
129 The population-based Reich-Patterson Fst is 0.33625.
130 130
131 </help> 131 </help>
132 </tool> 132 </tool>