|
2
|
1 <tool id="combineproballelecom" name="Combine read profile probabilities " version="2.0.0">
|
|
0
|
2 <description>from the same allele combination</description>
|
|
|
3 <command interpreter="python2.7">combinedprobforallelecombination.py $input > $output </command>
|
|
|
4
|
|
|
5 <inputs>
|
|
|
6 <param name="input" type="data" label="Select microsatellite length profile" />
|
|
|
7
|
|
|
8 </inputs>
|
|
|
9 <outputs>
|
|
|
10 <data name="output" format="tabular" />
|
|
|
11 </outputs>
|
|
|
12 <tests>
|
|
|
13 <!-- Test data with valid values -->
|
|
|
14 <test>
|
|
|
15 <param name="input" value="probvalueforhetero_out.txt"/>
|
|
|
16 <output name="output" file="combineprob_out.txt"/>
|
|
|
17 </test>
|
|
|
18
|
|
|
19 </tests>
|
|
|
20 <help>
|
|
|
21
|
|
|
22
|
|
|
23 .. class:: infomark
|
|
|
24
|
|
|
25 **What it does**
|
|
|
26
|
|
2
|
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.
|
|
0
|
28
|
|
|
29 **Citation**
|
|
|
30
|
|
|
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**
|
|
|
32
|
|
|
33 **Input**
|
|
|
34
|
|
|
35 The input format is the same as output from **Evaluate the probability of the allele combination to generate read profile** tool.
|
|
|
36
|
|
2
|
37 - Column 1 = location of STR locus.
|
|
|
38 - Column 2 = length profile (length of STR in each read that mapped to this location in comma separated format).
|
|
|
39 - Column 3 = motif of STR in this locus. The input file can contain more than three columns.
|
|
|
40 - Column 4 = homozygote/heterozygote label.
|
|
|
41 - Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
|
|
|
42 - Column 6 = Allele for most probable homozygote.
|
|
|
43 - Column 7 = Allele 1 for most probable heterozygote.
|
|
|
44 - Column 8 = Allele 2 for most probable heterozygote.
|
|
0
|
45 - Column 9 = Probability of the allele combination to generate given read profile.
|
|
|
46 - Column 10 = Number of possible rearrangement of given read profile.
|
|
|
47 - Column 11 = Probability of the allele combination to generate read profile with any rearrangement (Product of column 9 and column 10)
|
|
|
48 - Column 12 = Read depth
|
|
|
49
|
|
2
|
50 Only columns 2,3,4,7,8,11 were used in calculation.
|
|
0
|
51
|
|
|
52 **Output**
|
|
|
53
|
|
|
54
|
|
2
|
55 The output will contain the following header and columns
|
|
0
|
56
|
|
|
57 - Line 1 header: read_depth allele heterozygous_prob motif
|
|
|
58 - Column 1 = read depth
|
|
|
59 - Column 2 = allele combination
|
|
2
|
60 - Column 3 = probability to detect heterozygote of that allele combination
|
|
0
|
61 - Column 4 = motif
|
|
|
62
|
|
|
63
|
|
|
64
|
|
|
65
|
|
|
66 </help>
|
|
|
67 </tool>
|
