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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
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1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.1.0">
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2 <description>: Compute a fixation index score for each SNP</description>
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3
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4 <command interpreter="python">
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5 add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source" "$min_reads" "$min_qual" "$retain" "$discard_fixed" "$biased" "$output"
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6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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7 #set $arg = '%s:%s' % ($individual_col, $individual)
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8 "$arg"
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9 #end for
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10 </command>
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12 <inputs>
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13 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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14 <param name="p1_input" type="data" format="gd_indivs" label="Population 1 individuals" />
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15 <param name="p2_input" type="data" format="gd_indivs" label="Population 2 individuals" />
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17 <param name="data_source" type="select" format="integer" label="Frequency metric">
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18 <option value="0">sequence coverage</option>
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19 <option value="1" selected="true">estimated genotype</option>
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20 </param>
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22 <param name="min_reads" type="integer" min="0" value="0" label="Minimum total read count for a population" />
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23 <param name="min_qual" type="integer" min="0" value="0" label="Minimum individual genotype quality" />
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25 <param name="retain" type="select" label="If a SNP is below minimum">
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26 <option value="0" selected="true">skip SNP</option>
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27 <option value="1">set FST = -1</option>
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28 </param>
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30 <param name="discard_fixed" type="select" label="For SNPs that appear to be fixed across both populations">
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31 <option value="0">retain</option>
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32 <option value="1" selected="true">delete</option>
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33 </param>
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34
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35 <param name="biased" type="select" label="FST estimator">
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36 <option value="0">Wright's original definition</option>
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37 <option value="1">the Weir-Cockerham estimator</option>
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38 <option value="2" selected="true">the Reich-Patterson estimator</option>
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39 </param>
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41 </inputs>
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42
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43 <outputs>
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44 <data name="output" format="gd_snp" metadata_source="input" />
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45 </outputs>
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47 <tests>
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48 <test>
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49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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50 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
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51 <param name="p2_input" value="test_in/b.gd_indivs" ftype="gd_indivs" />
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52 <param name="data_source" value="0" />
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53 <param name="min_reads" value="3" />
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54 <param name="min_qual" value="0" />
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55 <param name="retain" value="0" />
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56 <param name="discard_fixed" value="1" />
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57 <param name="biased" value="0" />
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58 <output name="output" file="test_out/add_fst_column/add_fst_column.gd_snp" />
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59 </test>
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60 </tests>
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61
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62 <help>
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63
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64 **Dataset formats**
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65
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66 The input datasets are in gd_snp_ and gd_indivs_ formats.
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67 The output dataset is in gd_snp_ format. (`Dataset missing?`_)
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68
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69 .. _gd_snp: ./static/formatHelp.html#gd_snp
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70 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
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71 .. _Dataset missing?: ./static/formatHelp.html
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72
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73 -----
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74
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75 **What it does**
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76
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77 The user specifies a SNP table and two "populations" of individuals, both previously defined using the Galaxy tool to specify individuals from a SNP table. No individual can be in both populations. Other choices are as follows.
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78
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79 Frequency metric. The allele frequencies of a SNP in the two populations can be estimated either by the total number of reads of each allele, or by adding the frequencies inferred from genotypes of individuals in the populations.
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80
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81 After specifying the frequency metric, the user sets lower bounds on amount of data required at a SNP. For estimating the Fst using read counts, the bound is the minimum count of reads of the two alleles in a population. For estimations based on genotype, the bound is the minimum reported genotype quality per individual.
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82
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83 The user specifies whether the SNPs that violate the lower bound should be ignored or the Fst set to -1.
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84
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85 The user specifies whether SNPs where both populations appear to be fixed for the same allele should be retained or discarded.
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86
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87 Finally, the user chooses which definition of Fst to use: Wright's original definition, the Weir-Cockerham unbiased estimator, or the Reich-Patterson estimator.
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88
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89 A column is appended to the SNP table giving the Fst for each retained SNP.
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90
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91 References:
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93 Sewall Wright (1951) The genetical structure of populations. Ann Eugen 15:323-354.
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95 Weir, B.S. and Cockerham, C. Clark (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
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97 Weir, B.S. 1996. Population substructure. Genetic data analysis II, pp. 161-173. Sinauer Associates, Sundand, MA.
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99 David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes L. Price, and Lalji Singh (2009) Reconstructing Indian population history. Nature 461:489-494, especially Supplement 2.
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101 Their effectiveness for computing FSTs when there are many SNPs but few individuals is discussed in the following paper.
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102
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103 Eva-Maria Willing, Christine Dreyer, Cock van Oosterhout (2012) Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS One 7:e42649.
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105 -----
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106
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107 **Example**
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108
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109 - input, SNP table::
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110
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111 #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q",
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112 #"5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist","prim","rflp"],"dbkey":"canFam2",
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113 #"individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],
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114 #"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
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115 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
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
116 Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
117 Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
118 etc.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
119
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
120 - input, Population 1 individuals::
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
121
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
122 9 PB1
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
123 13 PB2
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
124
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
125 - input, Population 2 individuals::
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
126
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
127 17 PB3
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
128 21 PB4
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
129
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
130 - output (minimum read count of 3, discard fixed)::
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
131
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
132 Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0 0.1636
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
133 Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0 0.3846
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
134 etc.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 18
diff changeset
135
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
136 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
137 </tool>