Mercurial > repos > miller-lab > snp_analysis_conversion

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Bugfix from Belinda, in vcf2pgSnp.pl
author Cathy Riemer <cathy+hg@bx.psu.edu>
date Thu, 19 Mar 2015 12:06:34 -0400
parents 35c20b109be5
children
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3
edf12470a1a6 Bugfix from Belinda, in vcf2pgSnp.pl
Cathy Riemer <cathy+hg@bx.psu.edu>
parents: 2
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1 <tool id="vcf2pgSnp" name="VCF to pgSnp" version="1.1.0" hidden="false">
2
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2 <description>: Convert from VCF to pgSnp format</description>
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3 <command interpreter="perl">
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4 #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1
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5 #else #vcf2pgSnp.pl $inType.ind_column $input1 > $out_file1
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6 #end if
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7 </command>
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8 <inputs>
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9 <param format="vcf" name="input1" type="data" label="VCF dataset" />
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10 <conditional name="inType">
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11 <param name="how" type="select" label="How to treat individuals">
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12 <option value="all">Group all as a population</option>
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13 <option value="one">Do just one individual</option>
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14 </param>
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15 <when value="one">
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16 <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" />
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17 </when>
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18 <when value="all">
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19 <!-- do nothing -->
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20 </when>
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21 </conditional>
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22 </inputs>
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23 <outputs>
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24 <data format="interval" name="out_file1" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" />
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29 <param name="how" value="all" />
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30 <output name="output" file="vcf2pgSnp_output.pgSnp" />
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31 </test>
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32 </tests>
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33
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34 <help>
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35
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36 **Dataset formats**
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37
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38 The input dataset is in VCF_ format.
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39 The output dataset is pgSnp_. (`Dataset missing?`_)
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40
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41 .. _VCF: ./static/formatHelp.html#vcf
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42 .. _pgSnp: ./static/formatHelp.html#pgSnp
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43 .. _Dataset missing?: ./static/formatHelp.html
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44
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45 -----
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46
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47 **What it does**
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48
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49 This converts a VCF dataset to pgSnp format, using chromosome counts for
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50 the allele frequencies. If there is more than one column (individual)
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51 of SNP data, it can either combine all columns as a population, or just
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52 convert a single selected column.
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53
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54 -----
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55
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56 **Examples**
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57
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58 - input::
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59
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60 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48
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61 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48
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62 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48
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63 etc.
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64
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65 - output as a population::
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66
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67 chr1 13326 13327 G/C 2 7,1 0,0
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68 chr1 13979 13980 T/C 2 7,1 0,0
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69 chr1 30922 30923 G/T 2 4,4 0,0
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70 etc.
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71
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72 - output for column 10::
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73
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74 chr1 13326 13327 G 1 2 0
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75 chr1 13979 13980 T 1 2 0
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76 chr1 30922 30923 T 1 2 0
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77 etc.
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78
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79 </help>
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80 </tool>