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1 <tool id="combineproballelecom" name="Combine read profile probabilities " version="2.0.0">
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2 <description>from the same allele combination</description>
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3 <command interpreter="python2.7">combinedprobforallelecombination.py $input > $output </command>
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4
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5 <inputs>
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6 <param name="input" type="data" label="Select microsatellite length profile" />
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7
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="tabular" />
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11 </outputs>
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12 <tests>
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13 <!-- Test data with valid values -->
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14 <test>
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15 <param name="input" value="probvalueforhetero_out.txt"/>
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16 <output name="output" file="combineprob_out.txt"/>
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17 </test>
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18
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19 </tests>
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20 <help>
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21
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22
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23 .. class:: infomark
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24
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25 **What it does**
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26
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27 - This tool will combine the read profile probabilities for each allele combination in the input and calculates the probability to detect heterozygote for each allele combination and each depth.
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28
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29 **Citation**
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30
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31 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
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32
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33 **Input**
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34
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35 The input format is the same as output from **Evaluate the probability of the allele combination to generate read profile** tool.
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36
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37 - Column 1 = location of STR locus.
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38 - Column 2 = length profile (length of STR in each read that mapped to this location in comma separated format).
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39 - Column 3 = motif of STR in this locus. The input file can contain more than three columns.
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40 - Column 4 = homozygote/heterozygote label.
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41 - Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
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42 - Column 6 = Allele for most probable homozygote.
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43 - Column 7 = Allele 1 for most probable heterozygote.
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44 - Column 8 = Allele 2 for most probable heterozygote.
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45 - Column 9 = Probability of the allele combination to generate given read profile.
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46 - Column 10 = Number of possible rearrangement of given read profile.
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47 - Column 11 = Probability of the allele combination to generate read profile with any rearrangement (Product of column 9 and column 10)
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48 - Column 12 = Read depth
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49
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50 Only columns 2,3,4,7,8,11 were used in calculation.
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51
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52 **Output**
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53
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54
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55 The output will contain the following header and columns
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56
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57 - Line 1 header: read_depth allele heterozygous_prob motif
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58 - Column 1 = read depth
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59 - Column 2 = allele combination
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60 - Column 3 = probability to detect heterozygote of that allele combination
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61 - Column 4 = motif
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62
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63
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64
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65
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66 </help>
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67 </tool>
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