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comparison combineprobforallelecombination.xml @ 2:d5ed5c2e25c3 draft

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author arkarachai-fungtammasan
date Wed, 22 Apr 2015 12:48:40 -0400
parents 07588b899c13
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1:f2bab38e3cbd 2:d5ed5c2e25c3
1 <tool id="combineproballelecom" name="Combine probability to generate read profile " version="2.0.0"> 1 <tool id="combineproballelecom" name="Combine read profile probabilities " version="2.0.0">
2 <description>from the same allele combination</description> 2 <description>from the same allele combination</description>
3 <command interpreter="python2.7">combinedprobforallelecombination.py $input > $output </command> 3 <command interpreter="python2.7">combinedprobforallelecombination.py $input > $output </command>
4 4
5 <inputs> 5 <inputs>
6 <param name="input" type="data" label="Select microsatellite length profile" /> 6 <param name="input" type="data" label="Select microsatellite length profile" />
22 22
23 .. class:: infomark 23 .. class:: infomark
24 24
25 **What it does** 25 **What it does**
26 26
27 - This tool will combine probability that the allele combination can generated any read profile in the input. This is the last step to calculate probability to detect heterozygous for each allele combination and each depth. 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.
28 28
29 **Citation** 29 **Citation**
30 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** 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 32
33 **Input** 33 **Input**
34 34
35 The input format is the same as output from **Evaluate the probability of the allele combination to generate read profile** tool. 35 The input format is the same as output from **Evaluate the probability of the allele combination to generate read profile** tool.
36 36
37 - Column 1 = location of microsatellite locus. 37 - Column 1 = location of STR locus.
38 - Column 2 = length profile (length of microsatellite in each read that mapped to this location in comma separated format). 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 microsatellite in this locus. The input file can contain more than three column. 39 - Column 3 = motif of STR in this locus. The input file can contain more than three columns.
40 - Column 4 = homozygous/heterozygous label. 40 - Column 4 = homozygote/heterozygote label.
41 - Column 5 = log based 10 of (the probability of homozygous/the probability of heterozygous) 41 - Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
42 - Column 6 = Allele for most probable homozygous form. 42 - Column 6 = Allele for most probable homozygote.
43 - Column 7 = Allele 1 for most probable heterozygous form. 43 - Column 7 = Allele 1 for most probable heterozygote.
44 - Column 8 = Allele 2 for most probable heterozygous form. 44 - Column 8 = Allele 2 for most probable heterozygote.
45 - Column 9 = Probability of the allele combination to generate given read profile. 45 - Column 9 = Probability of the allele combination to generate given read profile.
46 - Column 10 = Number of possible rearrangement of 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) 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 48 - Column 12 = Read depth
49 49
50 Only column 2,3,4,7,8,11 were used in calculation. 50 Only columns 2,3,4,7,8,11 were used in calculation.
51 51
52 **Output** 52 **Output**
53 53
54 54
55 The output will contain the following header and column 55 The output will contain the following header and columns
56 56
57 - Line 1 header: read_depth allele heterozygous_prob motif 57 - Line 1 header: read_depth allele heterozygous_prob motif
58 - Column 1 = read depth 58 - Column 1 = read depth
59 - Column 2 = allele combination 59 - Column 2 = allele combination
60 - Column 3 = probability to detect heterozygous of that allele combination 60 - Column 3 = probability to detect heterozygote of that allele combination
61 - Column 4 = motif 61 - Column 4 = motif
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